tidal hydrodynamics and bedload transport in a shallow ......york, usa) provided a description of...

Tidal Hydrodynamics and Bedload Transport in a Shallow, Vegetated Harbor

(Stony Brook Harbor, Long Island, New York):

A Modeling Approach with Management Implications

A Thesis Presented

by

Nickitas Georgas

to

The Graduate School

in Partial Fulfillment of the

Requirements

for the Degree of

Master of Science

in

Marine Environmental Science

State University of New York

at Stony Brook

August 2001

ii

State University of New Yorkat Stony Brook

The Graduate School

Nickitas Georgas

We, the thesis committee for the above candidate for the

Master of Sciences Degree,

hereby recommend acceptance of this thesis.

Robert E. WilsonThesis Co-advisor, Associate Professor

Marine Sciences Research Center

Robert Lawrence SwansonThesis Co-advisor, Adjunct Professor

Director, Waste Reduction and Management Institute, Marine Sciences Research Center

Henry BokuniewiczProfessor


Dong-Ping WangProfessor


This thesis is accepted by the Graduate School

Dean of the Graduate School

iii

Abstract of the Thesis

Tidal Hydrodynamics and Bedload Transport in a Shallow, Vegetated Harbor

(Stony Brook Harbor, Long Island, New York):

A Modeling Approach with Management Implications

by

Nickitas Georgas

Master of Science

in

Marine Environmental Science

State University of New York

at Stony Brook

2001

A high-resolution numerical model for Stony Brook Harbor (Long Island, New

York, USA) provided a description of the tidal hydrodynamics and bedload transport

rates associated with localized dredging, under both neap and spring tide conditions. The

nonlinear hydrodynamic model, ADCIRC-2DDI, functioned effectively even under

extensive wetting and drying of the marsh islands and intertidal flats. The model results

were verified against sea level data recovered by three tide gauges.

Model and observations indicate strong flood-dominated tidal asymmetry inside

the harbor, with marked fortnightly variation. Although residual currents in the channels

are directed seaward, residual bedload transports exhibit marked flood-dominant behavior

inside the embayment. The low water level inside the embayment is elevated relative to

the low water in Smithtown Bay. The low water level inside the harbor is relatively

iv

constant, and appears to be independent of the exterior tidal forcing. Residual currents

and bedload vectors are directed seaward from the inlet mouth in Smithtown Bay due to

the formation of a strong ebb jet.

The effects of dredging were investigated through hypothetical alterations of the

existing bathymetry. Some effects of over-dredging Stony Brook Harbor’s channels to

3.7 m (12 ft) below MLW include: a) slower velocities in the dredged channels because

of the increase in cross-section, b) faster velocities in the non-dredged regions because of

the overall decrease in friction, c) less tidal asymmetry in the harbor’s interior primarily

because of the increase in channel depth and decrease in friction, d) less tidally-averaged

redistribution of sediment and shoaling inside the embayment, e) lowering of the low

water level at the head of the harbor, f) an increase in the exposure duration (drying) of

the harbor’s wetlands, g) an increase in the intertidal area (loss in subtidal area) of the

harbor, and possibly, h) higher rates of inward bedload transport after a storm.

(Table of contents)v

Table of Contents

Abstract iiiTable of Contents v List of Figures viiList of Tables xviiAcknowledgements

Chapter 1 Introduction and thesis objectives. 11.1. Objectives of this research. 11.2. Geographical setting. 21.3. Summary of previous research on tidal hydrodynamics and

bedload transport in Stony Brook Harbor (SBH).3

Chapter 2 Methods. 92.1. Field observations: sea level. 92.2. Model bathymetry.

Hydrographic Survey (2.2.1.).Use of tidal wetlands maps (2.2.2.).

101011

2.3. Hydrodynamic model.ADCIRC-2DDI (2.3.1.).ADCIRC-2DDI implementation (2.3.2.).Forcing, calibration, and verification (2.3.3.).

12121517

2.4. Analysis of model results.Tidal hydrodynamics (2.4.1.).Bedload transport (2.4.2.).Wetting and drying of intertidal areas (2.4.3.).

17171822

2.5. Investigation of dredging scenarios. 22

(Table of contents)vi

Chapter 3 Results and discussion. 253.1. Tide measurements.

Tidal datums and low waters at the head of the harbor (3.1.1.).Least squares harmonic analysis (3.1.2.).Implications for flood dominance (3.1.3.).Fortnightly variation in sea level asymmetry (3.1.4.).

2525273131

3.2. Hydrodynamic model evaluation. 333.3. Model results: Tidal hydrodynamics.

Sea level (3.3.1.). Time series (3.3.1.1.). Harmonic analysis (3.3.1.2.).Transient velocity (3.3.2.). Polar plots (3.3.2.1.). Description of the circulation in SBH (3.3.2.2.). Harmonic analysis (3.3.2.3.).Eulerian residual currents (3.3.3.). Residual currents (3.3.3.1.). Residual depth-averaged vorticity (3.3.3.2.).

3535353638383940404041

3.4. Model results: Bedload transport.Transient and residual bedload transport patterns (3.4.1).Residual bedload transport divergence (3.4.2).

444445

3.5. Model results: Inundation map of tidal flats. 473.6. Evaluation of response to first dredging scenario.

1st dredging scenario: Tidal hydrodynamics (3.6.1.).1st dredging scenario: Bedload transport (3.6.2.).1st dredging scenario: Inundation changes in intertidal areas (3.6.3.)

48485153

3.7. Evaluation of response to second dredging scenario.2nd dredging scenario: Tidal hydrodynamics (3.7.1.).2nd dredging scenario: Bedload transport (3.7.2.).2nd dredging scenario: Inundation changes in intertidal areas (3.7.3.)

54545558

Chapter 4 Summary and recommendations for future research. 60

4.1. Summary and conclusions. 60Observations (4.1.1.). 60Objective 1: Hydrodynamic model (4.1.2.). 60Objective 2: Bedload transport patterns (4.1.3.). 61Objective 3: Inundation maps of tidal flats and marshes (4.1.4.). 63 Objective 4: Evaluation of dredging scenarios (4.1.5.). 63

4.2. Recommendations for future research. 68

Figures 70Bibliography 148Table of acronyms 154Appendices 156

(List of Figures)vii

List of Figures

Figure Page1. Stony Brook Harbor (SBH), Long Island, NY, USA. Regional map, modified from

USGS St. James Quadrangle showing major locations in the harbor.70

2. Tide gauge and ground-truth locations: Stony Brook Yacht Club (SBYC), Smithtown

Bay (SB), head of the harbor (HoH), West Meadow Creek (WMC).71

3. Transects for the Stony Brook Harbor Hydrographic Survey (after Marcoe, 1999). The

original transects shown in the figure were expanded by Cademartori (2001) to include major intertidal regions and the two creeks.

72

4. Detail of the model domain as a mesh of linear finite elements. 73

5. Selected model stations along the three major flowways of Stony Brook Harbor

(Porpoise Channel line, Main Channel line, and West Meadow Creek line).74

6. Bathymetry of the major Stony Brook Harbor flowways along the line connecting their

deepest resolved points (Hydrography of the convection channels).6a (top left): Stony Brook Harbor bathymetry (m below MSL).6b (top): Porpoise Channel line and hydrography of its gorge.6c (bottom left): West Meadow Creek line and hydrography.6d (bottom): Main Channel line and hydrography of its gorge.

75

7. Sediment map. Distribution of sediment types across the model domain. Composite

map comprised by Smithtown Bay (from Knebel et al., 2000), Stony Brook Harbor (Park, 1985), and West Meadow Creek (Ericsson, 1997).

76

8. First dredging scenario: Reconfiguration of channels after dredging them to 3.7 m (12

ft) below MLW and after exp anding Porpoise Channel. The figure shows locations of the two channels based on the existing channel baselines.

77

9. Second dredging scenario: Reconfiguration of channels as in the first dredging

scenario and expanding Main Channel between Young’s and Horse Shoe Islands to meet Porpoise Channel.

78

10. Time series of high and low waters for the Smithtown Bay and head of the harbor tide

gauge stations for the period 08/15/00 – 09/14/00.79

11. Sea level time series from the West Meadow Creek (WMC) tide gauge. The 8-day

record starts at 08/15/00, 1624 UTC.80

12. Spring-Neap variation in sea level for Smithtown Bay (SB) and the head of the harbor

(HoH).Spring tide conditions: 8/30/00 – 8/31/00 (UTC)Neap tide conditions: 9/7/00 – 9/8/00 (UTC)12a (top): Spring-neap variation in Smithtown Bay.12b (bottom): Spring-neap variation in the head of the harbor.

81

13. Existing conditions: Sea level time series for selected model stations on the Porpoise

Channel line.13a (left): A diurnal cycle under neap tides.13b (right): A diurnal cycle under spring tides.

82

(List of Figures)viii

14. Existing conditions: Sea level time series for selected model stations on the Main


83

15. Existing conditions: M2 amplitude (m) for the three major waterways.

15a (top): M2 amplitude (m) along the Porpoise Channel line for both neap and spring tides.15b (middle): M2 amplitude (m) along the Main Channel line for both neap and spring tides.15c (bottom): M2 amplitude (m) along the West Meadow Creek line for neap tides.

84

16. Existing conditions: M2 phase (degrees) for the three major waterways.

16a (top): M2 phase (degrees) along the Porpoise Channel line for both neap and spring tides.16b (middle): M2 phase (degrees) along the Main Channel line for both neap and spring tides.16c (bottom): M2 phase (degrees) along the West Meadow Creek line for neap tides.

85

17. Existing conditions: M4 amplitude (m) for the three major waterways.

17a (top): M4 amplitude (m) along the Porpoise Channel line for both neap and spring tides.17b (middle): M4 amplitude (m) along the Main Channel line for both neap and spring tides.17c (bottom): M4 amplitude (m) along the West Meadow Creek line for neap tides.

86

18. Existing conditions: Z0 amplitude in meters (zero phase constituent, or average sea

level) for the three major waterways.18a (top): Z0 amplitude (m) along the Porpoise Channel line for both neap and springtides.18b (middle): Z0 amplitude (m) along the Main Channel line for both neap and spring tides.18c (bottom): Z0 amplitude (m) along the West Meadow Creek line for neap tides.

87

19. Existing conditions: Relative overtide growth (M4/M2 amplitude ratio) for the three

major waterways.19a (top): M4/M2 ratio along the Porpoise Channel line for both neap and spring tides.19b (middle): M4/M2 ratio along the Main Channel line for both neap and spring tides.19c (bottom): M4/M2 ratio along the West Meadow Creek line for neap tides.

88

20. Existing conditions: Relative phase (2Mº2-Mº4) for the three major waterways.

20a (top): 2Mº2-Mº4 along the Porpoise Channel line for both neap and spring tides.20b (middle): 2Mº2-Mº4 along the Main Channel line for both neap and spring tides.20c (bottom): 2Mº2-Mº4 along the West Meadow Creek line for neap tides.

89

(List of Figures)ix

21. Existing conditions: Representation of velocity time series in Smithtown Bay and Stony Brook Harbor Inlet through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.21a (top left): Current under a full diurnal neap tide cycle in a selected Smithtown Bay station (model node 53, 2000m northeast of station SB).21b (top): Current under a full diurnal spring tide cycle in a selected Smithtown Bay station (model node 53, 2000m northeast of station SB).21c (bottom left): Current under a full diurnal neap tide cycle in the inlet station I2 (see Figure 18 for reference).21d (bottom): Current under a full diurnal spring tide cycle in the inlet station I2.

90

22. Existing conditions: Representation of velocity time series in the Main Channel

through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.22a (top left): Current under a full diurnal neap tide cycle in the Main Channel station MC1 (see Figure 18 for reference).22b (top): Current under a full diurnal spring tide cycle in the Main Channel station MC1.22c (bottom left): Current under a full diurnal neap tide cycle in the Main Channel station MC3 (see Figure 18 for reference).22d (bottom): Current under a full diurnal spring tide cycle in the Main Channel station MC3.

91

23. Existing conditions: Representation of velocity time series in Porpoise Channel

through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.23a (top left): Current under a full diurnal neap tide cycle in Porpoise Channel station PC2 (see Figure 18 for reference).23b (top): Current under a full diurnal spring tide cycle in Porpoise Channel station PC2.23c (bottom left): Current under a full diurnal neap tide cycle in Porpoise Channel station PC4 (see Figure 18 for reference).23d (bottom): Current under a full diurnal spring tide cycle in Porpoise Channel station PC4.

92

24. Existing conditions: Representation of velocity time series at the head of the harbor

through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.24a (top left): Current under a full diurnal neap tide cycle at the head of the harbor station HoH1 (see Figure 18 for reference).24b (top): Current under a full diurnal spring tide cycle at the head of the harbor station HoH1.24c (bottom left): Current under a full diurnal neap tide cycle at the head of the harbor station HoH3 (see Figure 18 for reference).24d (bottom): Current under a full diurnal spring tide cycle at the head of the harbor station HoH3.

93

25. Model snapshot showing the maximum predicted pressure head between Stony Brook

Harbor’s interior and Smithtown Bay. Creation of the ebb jet.94

(List of Figures)x

26. Existing conditions: Depth-averaged velocity amplitudes of the M2 and M4 tidal

current constituents in m/sec along the Porpoise Channel line. Velocity amplitudes are represented by the velocity magnitudes of the major axis of the tidal ellipse of each Porpoise Channel station.26a (top): u(M2) amplitude (m/sec) in Porpoise Channel.26b (middle): u(M4) amplitude (m/sec) in Porpoise Channel.26c (bottom): u(M4)/u(M2) relative overtide velocity growth in Porpoise Channel.

95

27. Existing conditions: Depth-averaged velocity amplitudes of the M2 and M4 tidal

current constituents in m/sec along the Main Channel line. Velocity amplitudes are represented by the velocity magnitudes of the major axis of the tidal ellipse of each Main Channel station.27a (top): u(M2) amplitude (m/sec) in Main Channel.27b (middle): u(M4) amplitude (m/sec) in Main Channel.27c (bottom): u(M4)/u(M2) relative overtide velocity growth in Main Channel.

96

28. Existing conditions: Tidal residual current patterns (mean of depth-averaged velocity

through two semidiurnal tidal cycles). Spring tide simulation.97

29. Existing conditions: Volumetric time series of water stored inside Stony Brook

Harbor. Two days (under spring or neap forcing) are shown Volume of water is in cubic meters.29a (top): Time series of water volume stored inside Stony Brook Harbor (inside from the inlet) under neap tides.29b (bottom): Time series of water volume stored inside Stony Brook Harbor (inside from the inlet) under spring tides.

98

30. Stations selected for vorticity balance analysis at the head of the harbor (V1 through

V4). Contours show bathymetry and vectors indicate tidal residual currents.99

31. Existing conditions: Residual bedload transport (m2/day) in Stony Brook Harbor and

Smithtown Bay based on local sediment types.31a (left): Neap tides.31b (right): Spring tides.

100

32. Existing conditions: Residual bedload transport (m2/day) in Stony Brook Harbor and

Smithtown Bay for a uniform sand bed.32a (left): Neap tides.32b (right): Spring tides.

101

33. Existing conditions: Residual bedload transport divergence (mm/day) under neap tides

based on local sediment types.102

34. Existing conditions: Residual bedload transport divergence (mm/day) under spring

tides based on local sediment types.103

34a. Existing conditions. Detail of Figure 34. Residual bedload transport divergence

(mm/day) under spring tides based on local sediment types.104

35. Existing conditions: Residual bedload transport divergence (mm/day) under neap tides

for a uniform sand bed.105

(List of Figures)xi

36. Existing conditions: Residual bedload transport divergence (mm/day) under spring tides for a uniform sand bed.

106

37. Existing conditions: Residual bedload transport divergence at selected model stations. 107

38. Mean daily exposure (drying) of intertidal areas in hours/day. Existing conditions.

38a (left): Neap tide forcing.38b (right): Spring tide forcing.

108

39. First dredging scenario: Sea level time series for selected model stations on the

Porpoise Channel line.39a (left): A diurnal cycle under neap tides.39b (right): A diurnal cycle under spring tides.

109

40. First dredging scenario: Sea level time series for selected model stations on the Main


110

41. Comparison of sea level time series for selected model stations along the West

Meadow Creek line between existing conditions and the first dredging scenario.41a (left): Existing conditions.41b (right): First dredging scenario.

111

42. First dredging scenario: M2 amplitude (m) for the three major waterways. WMC was

closed for spring tides.42a (top): M2 amplitude (m) along the Porpoise Channel line for both neap and spring tides.42b (middle): M2 amplitude (m) along the Main Channel line for both neap and spring tides.42c (bottom): M2 amplitude (m) along the West Meadow Creek line for neap tides.

112

43. First dredging scenario: M2 phase (degrees) for the three major waterways. WMC was

closed for spring tides.43a (top): M2 phase (degrees) along the Porpoise Channel line for both neap and spring tides.43b (middle): M2 phase (degrees) along the Main Channel line for both neap and spring tides.43c (bottom): M2 phase (degrees) along the West Meadow Creek line for neap tides.

113

44. First dredging scenario: M4 amplitude (m) for the three major waterways. WMC was

closed for spring tides.44a (top): M4 amplitude (m) along the Porpoise Channel line for both neap and spring tides.44b (middle): M4 amplitude (m) along the Main Channel line for both neap and spring tides.44c (bottom): M4 amplitude (m) along the West Meadow Creek line for neap tides.

114

(List of Figures)xii

45. First dredging scenario: Z0 amplitude in meters (zero phase constituent, or average sea level) for the three major waterways. WMC was closed for spring tides.45a (top): Z0 amplitude (m) along the Porpoise Channel line for both neap and spring tides.45b (middle): Z0 amplitude (m) along the Main Channel line for both neap and spring tides.45c (bottom): Z0 amplitude (m) along the West Meadow Creek line for neap tides.

115

46. First dredging scenario: Relative overtide growth (M4/M2 amplitude ratio) for the three

major waterways. WMC was closed for spring tides.46a (top): M4/M2 ratio along the Porpoise Channel line for both neap and spring tides.46b (middle): M4/M2 ratio along the Main Channel line for both neap and spring tides.46c (bottom): M4/M2 ratio along the West Meadow Creek line for neap tides.

116

47. First dredging scenario: Relative phase (2Mº2-Mº4) for the three major waterways.

WMC was closed for spring tides.47a (top): 2Mº2-Mº4 along the Porpoise Channel line for both neap and spring tides.47b (middle): 2Mº2-Mº4 along the Main Channel line for both neap and spring tides.47c (bottom): 2Mº2-Mº4 along the West Meadow Creek line for neap tides.

117

48. First dredging scenario: Representation of velocity time series in the Main Channel

through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.48a (top left): Current under a full diurnal neap tide cycle in the Main Channel station MC1.48b (top): Current under a full diurnal spring tide cycle in the Main Channel station MC1.48c (bottom left): Current under a full diurnal neap tide cycle in the Main Channel station MC3.48d (bottom): Current under a full diurnal spring tide cycle in the Main Channel station MC3.

118

49. First dredging scenario: Representation of velocity time series in Porpoise Channel

through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.49a (top left): Current under a full diurnal neap tide cycle in Porpoise Channel station PC2.49b (top): Current under a full diurnal spring tide cycle in Porpoise Channel station PC2.49c (bottom left): Current under a full diurnal neap tide cycle in Porpoise Channel station PC4.49d (bottom): Current under a full diurnal spring tide cycle in Porpoise Channel station PC4.

119

(List of Figures)xiii

50. First dredging scenario: Representation of velocity time series in Smithtown Bay and Stony Brook Harbor Inlet through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the

at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.50a (top left): Current under a full diurnal neap tide cycle in a selected Smithtown Bay station (model node 53, 2000m northeast of station SB).50b (top): Current under a full diurnal spring tide cycle in a selected Smithtown Bay station (model node 53, 2000m northeast of station SB).50c (bottom left): Current under a full diurnal neap tide cycle in the inlet station I2.50d (bottom): Current under a full diurnal spring tide cycle in the inlet station I2.

120

51. First dredging scenario: Representation of velocity time series at the head of the harbor

through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.51a (top left): Current under a full diurnal neap tide cycle at the head of the harbor station HoH1.51b (top): Current under a full diurnal spring tide cycle at the head of the harbor station HoH1.51c (bottom left): Current under a full diurnal neap tide cycle at the head of the harbor station HoH3.51d (bottom): Current under a full diurnal spring tide cycle at the head of the harbor station HoH3.

121

52. First dredging scenario: Differences in tidal residual currents and water transport after

the implementation of the first dredging scenario. Neap tides. Difference of a property is defined here as the value of that property after dredging minus that property before dredging.52a (left): Differences in tidal residual current in m/sec (mean of depth-averagedvelocity through two semidiurnal tidal cycles). The colormap represents magnitude of difference in residual currents (m/sec). Vectors show magnitude and direction of differences.52b (right): Differences in tidal residual water transport in m2/sec. The colormap represents magnitude of difference in residual transport (m2/sec). Vectors showmagnitude and direction of differences.

122

53. First numerical experiment for the first dredging scenario: Residual bedload transport

(m2/day) in Stony Brook Harbor and Smithtown Bay based on local sediment types. 53a (left): Neap tides.53b (right): Spring tides.

123

54. Second numerical experiment for the first dredging scenario: Residual bedload

transport (m2/day) in Stony Brook Harbor and Smithtown Bay for a uniform sand bed.54a (left): Neap tides.54b (right): Spring tides.

124


divergence (mm/day) under neap tides based on local sediment types.125


divergence (mm/day) under spring tides based on local sediment types.126

(List of Figures)xiv

56a. First numerical experiment for the first dredging scenario. Detail of Figure 56.Residual bedload transport divergence (mm/day) under spring tides based on local sediment types.

127


transport divergence (mm/day) under neap tides for a uniform sand bed.128


transport divergence (mm/day) under spring tides for a uniform sand bed.129

59. First dredging scenario: Residual bedload transport divergence at selected model

stations.130

60. Mean expected daily increase in exposure duration (drying) of intertidal areas in

hours/day. First dredging scenario.60a (left): Neap tide forcing.60b (right): Spring tide forcing.

131

61. Second dredging scenario: Sea level time series for selected model stations on the

Porpoise Channel line.61a (left): A diurnal cycle under neap tides.61b (right): A diurnal cycle under spring tides.

132

62. Second dredging scenario: Sea level time series for selected model stations on the

Main Channel line.62a (left): A diurnal cycle under neap tides.62b (right): A diurnal cycle under spring tides.

133

63. Second dredging scenario: Relative overtide growth (M4/M2 amplitude ratio) for the

three major waterways. WMC was closed for spring tides.63a (top): M4/M2 ratio along the Porpoise Channel line for both neap and spring tides.63b (middle): M4/M2 ratio along the Main Channel line for both neap and spring tides.63c (bottom): M4/M2 ratio along the West Meadow Creek line for neap tides.

134

64. Second dredging scenario: Relative phase (2Mº2-Mº4) for the three major waterways.

WMC was closed for spring tides.64a (top): 2Mº2-Mº4 along the Porpoise Channel line for both neap and spring tides.64b (middle): 2Mº2-Mº4 along the Main Channel line for both neap and spring tides.64c (bottom): 2Mº2-Mº4 along the West Meadow Creek line for neap tides.

135

65. Second dredging scenario: Representation of velocity time series in the Main Channel

through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.122a (top left): Current under a full diurnal neap tide cycle in the Main Channel station MC1.122b (top): Current under a full diurnal spring tide cycle in the Main Channel station MC1.122c (bottom left): Current under a full diurnal neap tide cycle in the Main Channel station MC3.122d (bottom): Current under a full diurnal spring tide cycle in the Main Channel station MC3.

136

(List of Figures)xv

66. Second dredging scenario: Representation of velocity time series in Porpoise Channel through polar (radial) plots of depth-averaged velocity magnitude. The lines follow the tip of the velocity vector; the vector’s origin and the station’s position are at the center of the circle. 0 degrees is UTM83 East. Velocity magnitude in m/sec.66a (top left): Current under a full diurnal neap tide cycle in Porpoise Channel station PC2.66b (top): Current under a full diurnal spring tide cycle in Porpoise Channel station PC2.66c (bottom left): Current under a full diurnal neap tide cycle in Porpoise Channel station PC4.66d (bottom): Current under a full diurnal spring tide cycle in Porpoise Channel station PC4.

137

67. First numerical experiment for the second dredging scenario: Residual bedload

transport (m2/day) in Stony Brook Harbor and Smithtown Bay based on local sediment types.67a (left): Neap tides.67b (right): Spring tides.

138

68. Second numerical experiment for the second dredging scenario: Residual bedload

transport (m2/day) in Stony Brook Harbor and Smithtown Bay for a uniform sand bed.68a (left): Neap tides.68b (right): Spring tides.

139


transport divergence (mm/day) under neap tides based on local sediment types.140


transport divergence (mm/day) under spring tides based on local sediment types.141

70a. First numerical experiment for the second dredging scenario. Detail of Figure 70.

Residual bedload transport divergence (mm/day) under spring tides based on local sediment types.

142


transport divergence (mm/day) under neap tides for a uniform sand bed.143


transport divergence (mm/day) under spring tides for a uniform sand bed.144

73. Second dredging scenario: Residual bedload transport divergence at selected model

stations.145

74. Comparison of mean annual accreting volumes and accretion rates between the

existing conditions and the two dredging scenarios.74a (top): Mean annual accreting volume in significant shoaling areas.74b (bottom): Mean annual accretion rate in significant shoaling areas.

146

75. Mean expected daily increase in exposure duration (drying) of intertidal areas in

hours/day. Second dredging scenario.75a (left): Neap tide forcing.75b (right): Spring tide forcing.

147

(List of Figures)xvi

A-1-1. Temperature correction (calibration curve) of the Stony Brook Yacht Club tide gauge sensor.

158

A-1-2. Ground-truthing of the head of the harbor tide gauge. Regression between tide gauge

and shoreline-observed sea level at HoH.159

A-2-1. Stony Brook Harbor marshes identification map, based on NYS DEC digitized tidal wetlands maps superimposed on the USGS Quadrangle map.

163

(List of tables)xvii

List of Tables

Table Page1. Stony Brook Yacht Club (SBYC) tide gauge log (02/01/00 – 04/14/00). 9

2. Smithtown Bay (SB), head of the harbor (HoH), and West Meadow Creek

(WMC) tide gauge log (08/15/00 – 09/27/00).10

3. Model domain sediment types and bedload transport parameters. 20

4. Tidal datums for Smithtown Bay and the head of the harbor. 25

5. Astronomic constituents (least-squares results) extracted from the observed

time series in Smithtown Bay and the head of the harbor.28

6. Astronomic constituents (least-squares results) extracted from the observed

time series in West Meadow Creek and Stony Brook Yacht Club.30

7. Neap to spring tide variation in M2, M4, and tidal asymmetry. 32

8. Stony Brook Harbor model: Skill assessment 34

9. Residual vorticity analysis (depth-averaged vorticity balance) for head of the

harbor vorticity stations V1-4.43

10. Tidal characteristic numbers of bedload transport: Flood-to-ebb-ratio and net

transport. 1st and 2nd numerical experiments. Neap and spring tides.45


transport. 1st dredging scenario. For comparison with table 10 (existingconditions).

52


transport. 2nd dredging scenario. For comparison with tables 10-11.56

13. Significant (>0.1mm/day) shoaling areas, volume fluxes, shoaling rates, and

accreting sediment volumes.57

14. Comparison of mean annual accretion rate for significant shoaling areas

between the existing conditions and the two dredging scenarios.58

15. Comprehensive quantification of the dredging-induced alterations. 67

A-1-1. Post-calibration of the Stony Brook Yacht Club tide gauge. 157

A-2-1. Approximate acreage and mean depths of marshes, geographic regions and

water bodies relative to the project.162

Acknowledgements

I am very thankful to my advisors Drs. Robert E. Wilson and R. Lawrence

Swanson for their guidance and recommendations on this project, as well as to my

committee members, Drs. H. Bokuniewicz and D-P Wang for their comments and

assistance. I am grateful to the original developers of ADCIRC, Drs. R. Luettich, and J. J.

Westerink, for allowing me to use their hydrodynamic model. Special thanks go to the

Waterways Experiment Station / U.S. Army Corp of Engineers “team”, Drs. N. C. Kraus,

A. Militello, and M. Brown, for their recommendations on the design of the finite

element mesh, and the provision of pivotal references. Thanks to J. L. Hench for

providing ADSED.

The New York State Department of State is greatly acknowledged for providing

funds for this study. I am also thankful to the towns of Smithtown and Brookhaven, Long

Island, NY, and the Stony Brook Harbor Task Force for their encouraging support of the

project.

Gregg M. Cademartori, Keith E. Marcoe, and the faculty, staff, and students of

the Waste Reduction and Management Institute / MSRC are greatly acknowledged for

their assistance and support. Dr. L. E. Koppelman, the Windells family, the Stony Brook

Yacht Club, and Stony Brook Boat Works, provided access to field sites. The Smithtown

and Brookhaven constables helped with the deployment and recovery of the tidal gauges.

Last, but certainly not least, I thank Regan Elisabeth Greene, my family in

Greece, and my relatives in USA, for moral and emotional backing.

1

1. Introduction and thesis objectives.

1.1. Objectives of this research.

This thesis has four objectives. The primary objective is the description of the

tidal hydrodynamics and the processes controlling tidal asymmetry in Stony Brook

Harbor, Long Island, New York, U.S.A. (Figure 1). To address this objective, a high

resolution, two-dimensional, shallow water tidal model with wetting and drying was

applied to the harbor. The second objective is to use model results to develop a

description of spatial patterns of instantaneous and residual bedload transport within the

interior of the basin. A third objective involves the use of model results to describe the

patterns and duration of exposure (drying) of intertidal areas inside the harbor.

The fourth objective is to use the model to quantify dredging-induced changes in

the tidal hydrodynamics, bedload transport, and exposure of intertidal areas, using

bathymetry altered to simulate two proposed dredging scenarios. In recent years, the

harbor has been experiencing shoaling within its two channels, requiring frequent

dredging to access its four marinas (Smithtown Bay Yacht Club, Stony Brook Harbor

Yacht Club, Stony Brook Boat Works, and Long Beach Town Marina, Figure 1)

(Marcoe, 1999 and Cademartori, 2000). The results of the simulations provide new

insight into the effects of dredging on tidal asymmetry, tidal and residual circulation,

bedload transport and the spatial patterns of erosion and shoaling.

2

1.2. Geographical setting.

Stony Brook Harbor (Figure 1) is a shallow coastal embayment on Long Island’s

north shore covering 4.5 km2. It is subjected to the tidal forcing of Long Island Sound

through a single inlet with a minimum width of 75 m. The deepest point in the inlet is

approximately 10 m below Mean Sea Level. The narrow inlet restricts propagation of

wind waves generated in Long Island Sound to the harbor’s interior. Localized

production of wind waves inside the embayment is restricted due to the limited fetch

(Park, 1985).

The opening is bounded to the west by Long Beach spit and to the east by West

Meadow Beach spit. A two-channel system connects the inlet to the head of the harbor.

The northern Porpoise Channel accommodates about 70% of the tidal prism, while the

southeastern waterway, Main Channel (also known as Brookhaven Channel or Yacht

Club Spur), transports the remaining 30% of the prism (Park, 1985).

Approximately sixty-five percent of the harbor’s area has depths shallower than 1

m below Mean Sea Level. The channels are maintained at approximately 1.83 m (6 ft)

below Mean Low Water (MLW) by aperiodic dredging. The natural depth of the channels

should be approximately 60 cm (2 ft) below MLW (Cademartori, 2001).

A number of salt marsh islands and fringing marshes comprise the vegetated 28%

of the harbor’s area, and they are part of the protected tidal wetlands of Stony Brook

Harbor (SBH). This ecosystem has been designated a Significant Coastal Fish and

Wildlife Habitat by the New York State Department of State and a Significant Coastal

Habitat by the U.S. Fish and Wildlife Service. The vegetated intertidal areas that have

developed within the harbor are a haven for both endangered and threatened species

3

(Cademartori, 2000 and Cademartori, 2001).

West Meadow Creek (Figure 1) is a tributary that enters the northeast corner of

the harbor behind West Meadow Beach. Stony Brook Creek is a second tributary that

enters approximately midway down Main Channel (Figure 1). The two creeks and a

number of freshwater springs situated at the head of the harbor represent a small fresh

water source of less than 1% of the total tidal prism (Robbins, 1977). In such an

environment, density driven circulation as well as motion due to direct wind forcing is

considered insignificant relative to the barotropic tidal motion. The latter is largely

dominated by the tidal signal, channel and harbor geometry, bottom topography and

friction (Aubrey, 1986). It should be noted however that Long Island’s strong

northeasterly storms (“Nor’easters”) have a large impact on the hydrodynamics and

particularly the bedload sediment transport in the embayment.

1.3 Summary of previous research on tidal hydrodynamics and bedload

transport in SBH.

Marcoe (1999) used a 2D hydrodynamic model [RMA2, US Army Corp of

Engineers (1993)] to assess the impacts of channel dredging on the tidal hydrodynamics

of SBH. His simulations indicated the large ratio of tidal amplitude to channel depth to be

primarily responsible for the flood-dominant asymmetry observed inside the harbor.

Simulations for local dredging operations in Main Channel (Figure 1) indicated minimal

impact on tide range and phase lag within the harbor. He hypothesized that dredging-

induced local changes of the channel currents could be very important in the prediction of

sediment transport patterns inside the harbor. His simulations pointed to the importance

4

of small-scale residual current patterns produced through rectification of the transient

currents. His simulations did not, however, extent to bedload transport, and the wetting

and drying capabilities of his model were limited. This study addresses these issues.

Marcoe (1999) collected and analyzed sea level observations as part of his study.

Mean monthly tidal range in Smithtown Bay, just outside the inlet, was found to be 2.13

m with maximum spring tidal range of 3.0 m (Marcoe, 1999). The tidal range decreased

further from the inlet mouth to 1.83 m at the Stony Brook Yacht Club and to 1.77 m at

the head of the harbor (Marcoe, 1999). Cademartori (2001) conducted a high water

survey and found that high waters relative to the National Geodetic Vertical Datum in all

three locations were within 3 cm of each other. Thus, most of the decrease in tidal range

is associated with a rise of the Mean Low Water (MLW) level inside the embayment

relative to Smithtown Bay (Cademartori, 2001). Mean Sea Level (MSL) and Mean Tide

Level (MTL) in Smithtown Bay, outside the shallow harbor, are approximately equal as

in a classic undistorted semidiurnal tide. Tidal asymmetry inside the harbor causes MSL

to be lower than MTL by approximately 10 cm at the harbor’s head (Marcoe, 1999).

The tide in SBH is semidiurnal with the M2 principal lunar constituent being the

greatest semidiurnal component, although the principal solar, S2, and the larger lunar

elliptic, N2, are also present (Brown, 1985). Interaction of these constituents leads to

appreciable fortnightly and monthly modulation of the semidiurnal tide which in turn

leads to modulation of the overtide (quarter-diurnal) response (Marcoe, 1999). Harmonic

overtides can be generated by the three nonlinear terms in the shallow water equations:

the nonlinear continuity term, the inertial (advective) term in the momentum equation,

and the nonlinear friction term. Even harmonics (e.g., M4) produce asymmetry related to

5

flood- or ebb-dominant behavior. The term asymmetry refers specifically to the unequal

duration of the rise and fall of the tide, and the associated unequal magnitude of the

flood- and ebb-directed tidal currents. Odd harmonics (e.g., M6) are thought to produce

symmetric effects without distorting the tidal wave profile (Parker, 1991). The zero-order

effect of nonlinearities in SBH is the aforementioned MSL rise inside the embayment.

The asymmetry in both the duration of the rise and fall of the tides and the

magnitude of the ebb and flood currents inside embayments with semidiurnal tides is

governed by the phase difference 2M2o - M4

o (i.e., twice the phase of the principal

semidiurnal constituent, M2, minus the phase of M4, its main overtide), and the amplitude

ratio (M4/M2). The greater the amplitude ratio M4/M2 is, the more nonlinear the response

and the more potentially distorted (asymmetric) the tide. The phase difference 2M2o - M4

o

in elevation is used to characterize the type of asymmetry in the currents (ebb-dominant

or flood-dominant). If this value is between 0º and 180º, the harbor is considered flood-

dominant (Speer and Aubrey, 1985). For the head of SBH, Marcoe (1999) observed 2M2o

- M4o equal to 60.1º and M4/M2 equal to 0.169, indicating strong, flood-dominant

conditions.

Park (1985) observed maximum flood currents just inside the inlet mouth equal to

1.7 m/s, while the maximum ebb current was only 1.2 m/s. In 1940, for the same location

and a neap tide, Suffolk County measured 1.8 m/s and 1.5 m/s for maximum flood and

ebb currents respectively while a more recent (1995) survey on a spring tide measured

current maxima of 2.2 m/s and 1.7 m/s for flood and ebb, respectively. The asymmetric

pattern of higher maximum flood currents than maximum ebb currents was observed at

three more stations, at the Main Channel, at Porpoise Channel and at a southern station

6

(Park, 1985), with a generally decreasing trend in current magnitude away from the inlet

(Bowman, 1989).

Brown (1985) used harmonic and spectral analyses to describe the asymmetrical

tidal signal inside SBH. Friedrichs and Madsen (1992) applied a 1-D, frictional model

with no advection (zero-inertia) to SBH and contrasted their results with observations by

Park (1985). Results from their zero-inertia model correlated well with the observations

from SBH, confirming the conclusions of Park (1985) and Brown (1985) that the

dynamic balance associated with the harbor’s flood-dominant behavior is primarily that

between sea level pressure and bottom friction.

The zero-inertia approximation leads to depth and storage dependent flood crest

propagation and dissipation, and accounts for the asymmetric rise and fall typical of flood

waves. Friedrichs and Madsen (1992) acknowledged that their zero-inertia analysis was

“limited to nonlinearities with a basin-wide character and did not consider advective

nonlinearities typically localized to smaller geometric features such as inlets, sand banks,

or channel meanders.” Simulations by Marcoe (1999) indicated that both instantaneous

and residual currents with the tidal signal removed within the interior of SBH are in fact

strongly influenced by the interaction of the tidal streams with the local bathymetry

through nonlinear mechanisms. A fully nonlinear model is required to simulate these

processes. It is important to resolve localized nonlinearities in the currents to effectively

infer bedload transport patterns.

Bowman (1989) used Lagrangian drifters and a finite difference model with a 70

m grid dimension to estimate residual drift currents in SBH. His results indicated that the

general residual current structure tended to move the drifters out of the harbor, an

7

observation that seems inconsistent with that of Park (1985), of higher maximum flood

than ebb currents and the discussion of the bay’s flood dominant behavior by Marcoe

(1999). It will be shown in this thesis that there is no inconsistency between these results

because the maximum rather than residual currents control the residual bedload transport

patterns inside SBH. Apart from Bowman’s (1989) work, the residual transport patterns

within SBH have not previously been described.

There is strong indication that, within SBH, flood-dominant tidal current

asymmetry contributes to the net import of bedload into the southern part of the basin

[Park, (1985), Marcoe, (1999)]. Greater flood than ebb currents in the harbor’s interior

tend to transport sediment in a net direction toward the head of the harbor, causing the

embayment to act as a sediment sink. The primary parameter controlling the flood-

dominant behavior of the shallow SBH basin is the channel depth [e.g., Speer and Aubrey

(1985), Friedrichs and Madsen (1992)]. It will be shown, that the proposed over-dredging

scenarios will lower the intensity of flood-dominant bedload transport within the interior

of the basin primarily by decreasing the asymmetry between flood and ebb friction. A

secondary controlling parameter for the hydrodynamics in SBH is intertidal storage, an

issue that was resolved by the wetting and drying capabilities of the model used in this

study.

Park (1985) used a 1D box model with 36 cells to predict tidal hydraulics and

sediment transport patterns in the harbor channels. He took observations of sea level and

currents in order to force and verify his model, and he assessed the effects of six dredging

plans for the Main and inlet channels on sea level, currents, and sediment transport. He

found that the predicted sediment transport rates, integrated over two spring-neap cycles

8

were all flood-oriented. Zarillo and Park (1987) found that the predicted net sediment

transport patterns based on Park’s (1985) coarse model agreed well with observed

conditions, showing convergence of transport in shoaling areas and divergence in

erosional areas. For example, a large scour hole at the harbor inlet is located where net

sediment transport was predicted to diverge. The very high resolution, fully nonlinear

model used in the present thesis enables description of bedload transport patterns in much

greater detail.

9

2. Methods.

2.1. Field observations: sea level.

Observations of sea level were collected from three sites in SBH using 100 PSIA

pressure sensors. Two gauges were deployed at sites used by Marcoe (1999), one at

Smithtown Bay (SB) and the other at the head of the harbor (HoH). Additional gauges

were deployed in West Meadow Creek (WMC) and the Stony Brook Yacht Club (SBYC)

(Figure 2). Tables 1 and 2 show instrument deployment histories. The influence of

barometric pressure was removed from sea level with the use of available data from a

gauge at Shinnecock Bay.

SBYC tide gauge Date Time RemarksFirst deployment 02/01/00 1422 EST First tide gauge deployed.First turnaround 02/17/00 1434 EST Gauge out of the water. Checked.Second deployment 02/17/00 1540 EST Gauge back in the water.Second turnaround 03/02/00 1403 EST Gauge out of the water. No record found.Third deployment 03/03/00 1548 EST A new tide gauge was deployed.

Retrieval 04/14/00 1538 EDT Retrieved data found to be inconsistent with ground truth observations. (*)

(*) Ground truth observations were taken from a staff fixed on the same dock pile as the tide gauge, situated in SBYC.Appendix A-1 includes a comparison of tide gauge and ground truth data for SBYC.

Table 1. Stony Brook Yacht Club (SBYC) tide gauge log (02/01/00 – 04/14/00)

10

SBtide gauge Date Time

(GMT) Easting Northing Latitude Longitude

Deployment 08/15/00 1651 655142 4533507 40 56 16.7 73 09 25.5 Retrieval 09/27/00 1412 655172 4533233 40 56 07.8 73 09 24.4

HoHtide gauge Date Time


Deployment 08/15/00 1542 653484 4529894 40 54 20.1 73 10 39.6 Check 08/22/00 2123 653484 4529894 40 54 20.1 73 10 39.6 Retrieval 09/27/00 1708 653487 4529880 40 54 20.3 73 10 39.4

WMCtide gauge Date Time


Deployment 08/15/00 1622 656605 4534340 40 56 42.7 73 08 22.2 Check 08/22/00 2231 656605 4534340 40 56 42.7 73 08 22.2 Retrieval 09/27/00 N/F (*) N/F N/F N/F N/F

(*) The WMC tide gauge is reported missing since 09/27/00 (Not Found).Note: Easting and Northing are Universal Transverse Mercator (UTM) coordinates of the North American Datum of 1983 (NAD83)

Table 2. Smithtown Bay (SB), head of the harbor (HoH), and West Meadow Creek(WMC) tide gauge log (08/15/00 – 09/27/00)

Local tidal datums were calculated based on a month’s worth of data, and sea

level observations were subject to least-squares harmonic analysis. The objective was to

extract the major diurnal, semidiurnal and overtide components under spring and neap

tide conditions to force, calibrate, and verify the hydrodynamic model.

2.2. Model bathymetry.

2.2.1. Hydrographic survey.

A high-resolution hydrographic survey of SBH had been completed on

01/11/00 (Cademartori, 2001). This survey (Figure 3) included bathymetry from Stony

Brook and West Meadow Creeks, as well as from major intertidal areas at the sites of

11

southern Young’s Island and northern Horse Shoe Island. The survey was conducted

around high waters allowing the inclusion of intertidal areas. Soundings were reduced to

MLW. The datum used for the model’s bathymetry was MSL to allow for easier

description of the model’s tidal constituents.

Model computational stability improves as the open boundary is moved

away from the restricted inlet. Open ocean boundaries need to be sufficiently far from the

coastal area of interest to avoid artificial reflection or inaccurate interaction of the ebb-

flow-generated jet stream with the forcing boundary [Blain et al. (1995), and Militello

(1998)]. Therefore, the bathymetry was extended to the outer boundary of SB (the line

connecting Eaton’s Neck to the West and Crane Neck to the East). This was done by

merging the SBH hydrographic survey data with SB depths extracted from the available

National Oceanic and Atmospheric Administration (NOAA) database. The SB data were

corrected to MSL from their MLW datum (Adams, 1942).

2.2.2. Use of tidal wetlands maps.

In order to effectively simulate wetting and drying of intertidal areas

inside SBH and to assess possible differences in the inundation duration of marshes after

channel dredging, all possible wetting and drying areas were included. In an estuary with

extensive intertidal shoals and mudflats, lack or improper representation of these areas

can be a source of significant modeling errors (e.g. Kuo and Park, 1995, Aubrey and

Speer, 1985). Direct measurement of the intersection of the required tidal datums of

Mean High Water (MHW) and Mean Higher High Water (MHHW) with the land surface

was impractical (Marmer, 1951, Hawkes, 1966, Garretson, 1968, Swanson, 1974) and

12

beyond the scope of this work. Thus, depths below and elevations above MSL in

intertidal areas not directly included in the hydrographic survey were inferred from marsh

vegetation maps.

Six tidal wetland maps (Nos. 652-528, 652-530, 654-528, 654-530, 654-

532, 656-532) created by the New York Department of Environmental Conservation

(1974) were digitized. The boundary between low (Spartina alterniflora) and high

(Spartina patens) marsh was drawn and used as a MHW contour. The landward boundary

of the high marsh was used to infer the MHHW contour.

The finite element grid representing the model domain is shown in Figure

4. The resolution varies from approximately 1,000 m at the SB forcing boundary to 25 m

in the SBH inlet, to approximately 5 m within certain areas of WMC. It increases to

approximately 75 m in the inner part of SBH. Transition from large to small elements had

to be gradual throughout the domain to avoid continuity problems (Donnell et al., 1996).

The maximum number of neighboring elements was limited to seven, and minimum

element angle was 30° to minimize computational errors related to water conservation

(Militello, 1998).

2.3. Hydrodynamic model.

2.3.1. ADCIRC-2DDI.

The bathymetric data were imported into commercial gridding software

[BOSS Surfacewater Modeling System Version 7.0; Boss Intl. and Brigham Young

University (2000)] to create a computational mesh of Finite Elements (FE) (Figure 4).

The FE model used for the simulation was ADCIRC-2DDI (Two Dimensional, Depth-

13

Integrated, Advanced Circulation Model, Luettich et al., 1992), Version 34-20

(copyrighted in 1999). The model solves the shallow water equations using the

generalized wave continuity equation (GWCE) form, and it includes nonlinear

acceleration and finite amplitude terms as well as the standard quadratic parameterization

of bottom friction. Thus, the model’s formulation included all nonlinear terms that

contribute to the creation of overtides and tidal asymmetry.

ADCIRC-2DDI is based on the two-dimensional, depth-integrated, shallow-water

equations:

( ) ( )∂η∂

∂∂

∂∂t

uHx

vHy

+ + = 0 (1)

uHvuC

Hxg

vfyuv

xuu

tu

Dx

2/122

0

)()( +−

′+−

=−∂

++

ρητ

∂∂η

∂∂∂

∂∂

(2)

vHvuC

Hyg

ufxvu

yvv

tv

Dy

2/122

0

)()( +−

′+−

=+++

ρητ

∂∂η

∂∂

∂∂

∂∂

(3)

where u v, are the depth-averaged velocities in the x and y directions, H is the total

instantaneous depth of the water column ),,(),(),,( tyxyxhtyxH η+= , h is the

bathymetric depth below MSL, η is the free surface elevation, yx ,τ ′ is the surface wind

stress in the x or y direction, DC is the quadratic drag coefficient, f the Coriolis

parameter, 0ρ is the water density, and g the acceleration of gravity. Equation (1) is the

shallow water continuity equation, while equations (2) and (3) are the shallow-water

14

momentum equations for the x and y directions respectively.

The Generalized Wave Continuity Equation (GWCE) solved by ADCIRC

in conjunction with the shallow water momentum equations (2 and 3) is used to avoid

numerical problems using a Galerkin finite element scheme. It is obtained by taking the

total derivative of the continuity equation and substituting the momentum equation to the

resulting expression (Westerink et al., 1992). Finally, the original continuity equation is

added, multiplied by a weighting factor, ô0, which controls the balance between primitive

and wave continuity formulations (Blain et al., 1995). The numerical method for

integrating the GWCE and the companion momentum equations is described in a number

of publications (e.g. Westerink et al., 1992, Luettich et al., 1992, Westerink et al., 1993,

Blain et al., 1995).

Lynch and Gray (1979) discussed the computational advantages of models

that solve a wave continuity equation like the GWCE. One of these features is the

suppression of short wavelength (2Äx) oscillations without the use of artificial damping

(see also Goutal, 1989). Use of the depth-averaged-velocity form of the momentum

equations, also circumvents divisions of transport by depth to obtain velocities and avoids

the divisions by zero that could arise in drying regions (Hervouet and Janin, 1994).

The finite element technique offers the flexibility needed to resolve

shallow water processes in the limited domain of SBH. Such an unstructured mesh is a

major asset in this study. Considerable grid refinement is required proceeding landward

from the open boundary to accurately resolve the spatial structure in both tidal current

and elevation in the entire domain. In shallow water, both propagation speed and tidal

wavelength become increasingly sensitive to bathymetry in terms of their influence on

15

surface elevations and currents (Westerink et al., 1992). Thus, large bathymetric

gradients as in the channels need to be sufficiently resolved.

2.3.2. ADCIRC-2DDI implementation.

The two-dimensional formulation of ADCIRC was used instead of a three-

dimensional version. Comparisons between these 2D and 3D models for computing

shallow water tides in a friction-dominated tidal embayment, such as SBH, have shown

that there are no important differences in the results (Grenier et al., 1993).

The assumptions and simplifications under which ADCIRC-2DDI ran for

both neap and spring tide forcing are summarized below:

• Evaporation, precipitation, groundwater, and freshwater input are

neglected.

• Changes in bathymetry within the run time (shoaling or scouring of

the bed) are neglected.

• No direct wind forcing, or wave radiation stress was included.

• Spatially uniform phase and amplitude sea level forcing were

assigned on the SB boundary.

• Differences between HW tidal datums and vegetation zonation

inside SBH are hydrodynamically insignificant.

The Coriolis force was included in the model although its effects inside

SBH are minimal. A lateral eddy diffusion term ),( yx DDDr

was included in the right hand

side of the momentum equations. The eddy viscosity coefficient, Eh, was spatially

homogeneous and isotropic. The coefficient was kept to a relatively small value (1.5

m2/s) in all model runs to improve stability to the numerical scheme without sacrificing

16

the accuracy of the model. This eddy viscosity value was lower than that used in

modeling tidal embayments of similar scales [e.g. Inoue and Wiseman (2000)].

The bottom shear stress in the momentum equations was represented using

the standard nonlinear quadratic form. In non-vegetated areas the drag coefficient, CD,

was set to the constant value of 0.002. In vegetated intertidal areas (marshes) the drag

coefficient was adjusted for vegetated resistance to a value of 10 [Tickner (1957), Reid

and Whitaker (1976), Tai and Fang (1995)].

The boundary condition (BC) imposed on all land boundaries (including

the islands) of the domain was that of no-normal flow. This BC set the velocity

component normal to the shoreline to zero if it did not satisfy the criterion for shoreline

advance (normal velocity component > 3 cm/s). According to Westerink et al. (1994),

artificial 2Äx oscillations would be created by this BC in a finite element model solving

the primitive continuity equation but they are avoided by the use of the GWCE in

ADCIRC.

The Courant number stability condition requires that, throughout the

computational domain, the ratio between the element size Äx and the timestep Ät, should

be greater than the shallow water wave celerity c. This condition sets a limit on the

maximum timestep allowed for convergent solutions of linear equations; Ät can be

constrained to even lower values if nonlinear terms are included in the governing

equations as in the present case. In this model, the Courant stability criterion translated

into a timestep of only 0.6 s.

17

2.3.3. Forcing, calibration and verification.

The model was forced on the open ocean boundary with the elevation

boundary conditions recovered from the SB tide gauge (Figure 2). Tidal forcing was

assigned to be uniform across the boundary. ADCIRC was run under both neap and

spring tide conditions to represent the two extremes in tidal forcing. Each run lasted four

simulation days. An initial ramping, spin-up period of half a day was allowed, to avoid

problems with short-period gravity modes (Westerink et al., 1992). After a subsequent

one-and-a-half-day period allotted for stabilization of periodic results, model output was

stored at ten-minute intervals for the third and fourth simulation days.

The model’s initial runs were calibrated against elevation data recovered from the

HoH gauge (Figure 2) both for semidiurnal and quarter-diurnal amplitude and phase.

Measurements from the WMC and SBYC tide gauges (Figure 2), as well as reported field

observations by Marcoe (1999) were compared with the simulated results for model

verification.

2.4. Analysis of model results.

2.4.1. Tidal hydrodynamics.

Sea level results from the calibrated model were analyzed for diurnal,

semidiurnal and overtide components using the least-squares technique described by

Lewis and Noye (1999). This technique has the capability of performing least-squares

harmonic analysis at partially dried areas where cropped (partially dried and therefore

discontinuous) time series occur. The expected accuracy for the tidal constituents

presentation was ±0.6 cm based on the tide gauge precision.

18

Three longitudinal transects were chosen to facilitate the discussion of

model results (Figure 5). They run along the harbor’s three major channel axes (Porpoise

Channel, Main Channel, and WMC). Model bathymetry along these transects is shown in

Figure 6. Least squares results (M2, M4, and Z0) as well as tidal asymmetry parameters

(M4/M2 and 2M2o - M4

o) were obtained for elevation along these transects.

For the calculation of residuals the output of the model was averaged at

each mesh node over two semidiurnal cycles. Thus, for example, the residual currents in

the harbor under both neap and spring forcing were calculated by averaging the

instantaneous currents recorded in the model output every 10 min over two semidiurnal

cycles (to include the diurnal modulation).

2.4.2. Bedload transport.

Transient bedload transport patterns were calculated from model results

using a modified Meyer-Peter and Müller (1948) formula (Chanson, 1999):

( ) 23

0

03

)1(4

)1( ⎥⎦

⎤⎢⎣

⎡−−

−=s

ts gds

gdsqρ

ττ vvv (4)

where ),( yx qqqv is the bedload transport vector in (x,y) directions, ),( ,0,00 yxτττv is the bed

shear stress, tτv is the threshold shear stress for initiation of bedload motion at the

direction of τv , g is the acceleration of gravity, sd is the sediment grain size (or diameter),

and s is the ratio between the density of sediment sρ and that of water 0ρ .

19

The density of sediment sρ was assumed to be close to that of quartz, or

2.65 g/cm3 (Miller et al., 1977). The bed shear stress is assumed to have the following

relationship to velocity (Kraus, 1998):

200 vCD

vv ρτ = (5)

where, CD is the bottom drag coefficient. A uniform value of 0.002 was used. The

velocity in equation (5) is usually interpreted as the 1-m-above-bed velocity (Savvidis,

2000) or the mean maximum velocity (Kraus, 1998); here, it was assumed to be equal to

the depth-averaged velocity of the model output taken at 10-min intervals.

The threshold shear stress (or, equivalently, threshold velocities defined as

( )Dtt Cv 0/ ρτ≡ ) depends on the sediment type. Two numerical experiments were

conducted for bedload transport calculations based on different sediment characteristics

and, thus, sediment thresholds. In both experiments, different sediment types were

assumed to be “well-sorted” with unskewed distributions, and degradation and

aggradation processes are neglected (Chanson, 1999).

The first numerical experiment was based on the actual sediment types of

the region of interest as shown in Figure 7. The map shown is a composite of three

different sediment maps [SB from Knebel et al. (2000), SBH from Park (1985), and

WMC from Ericsson (1997)].

Table 3 (next page), in combination with the Wentworth sediment

classification scale, were used to calculate:

the Yalin parameter 2

3)1(ν

sgds −≡Ξ , (6)

20

the Shields sediment threshold criterion,

( ) ss

tt gd0ρρ

τθ

−= , (7)

and, finally, through equation (7), the threshold shear stress needed for initiation of

sediment motion.

The Shields threshold criterion in Table 3 was read from a modified

Shields curve presented in Miller et al., (1977), given the Yalin parameter for a specific

sediment type. Note that this modified Shield’s curve [Miller et al., (1977)] should be

valid for all sediment types present since they do not include cohesive sediment of less

than 20 ì m diameter (Cacchione and Drake, 1986). The viscosity of water ν in equation

(6) was set equal to 0.01 cm2/s, its value for water of 20 ºC.

Sediment types

Mean(~median)

diameter, dmeters (m)

Yalinparameter

Ξ

Shieldsthresholdcriterion

tθ

Thresholdshear

stress, tτkg/m/s2

Thresholdvelocity,

tvm/s

Silt 2.20x10-5 0.415 0.1480 0.0527 0.16 Sand-silt-clay & plant matter 5.13x10-5 1.476 0.0933 0.0774 0.20

Silty sand 9.38x10-5 3.652 0.0676 0.1026 0.23 Very fine and silty sand 1.56x10-4 7.858 0.0562 0.1421 0.27

Sand 3.13x10-4 22.225 0.0427 0.2160 0.33 Medium and fine sand 3.75x10-4 29.216 0.0398 0.2416 0.35

Gravelly, very coarse sand, and cobbles

1.25x10-3 177.804 0.0316 0.6394 0.57

Gravel 1.10x10-2 4641.576 0.0479 8.5287 2.07

Table 3. Model domain sediment types and calculated bedload transport parameters.

21

The second numerical experiment for bedload transport involved a more

conservative approach; a uniform sediment type was prescribed for the whole domain,

neglecting any spatial variations. The sediment type used was sand (as in Table 3),

primarily to address questions regarding the bedload transport of the lighter than gravel

sediment fraction. This experiment is more representative of the situation following a

storm when material is deposited in the inlet. During storms, erosion of the sand bluffs in

SB occurs and longshore transport delivers this material to the harbor entrance.

After bedload transport was calculated for each numerical experiment,

bedload transport fluxes were calculated across transects (e.g., across the inlet throat) and

then they were time-integrated during periods of flood and ebb. Fry and Aubrey (1990)

used the ratio between flood-directed and ebb-directed bedload transport to characterize

asymmetry patterns in the transient field. This ratio is defined by:

qdtflood

qdtebb

∫

∫ (8)

where q is the bedload transport along the main flood-ebb axis in units of m2. This ratio

was calculated and integrated across three transects: at the inlet, at Porpoise Channel and

at Main Channel.

The transient bedload patterns were averaged to calculate the residual

bedload transport vectors. The divergence of these vectors was computed and was

superimposed on a map to identify possible patterns of erosion (bedload divergence) or

accumulation (bedload convergence). The time dependent bed elevation conservation

22

equation (Exner continuity equation) is described by Park (1990), and is modified here

from Hench and Luettich (2000):

( )thq

∂∂λν−=⋅∇ 1rr

(9)

where νλ is the bed porosity, assumed equal to 0.4 for well sorted quartz sediment with

no aggradation or degradation. Equation (9) indicates that a divergent bedload transport

field (r r∇ ⋅ >q 0 ) will tend to erode the bed over time, creating a deeper water column

∂∂ht

>⎛⎝⎜

⎞⎠⎟

0 . A negative bedload divergence of bedload transport will create a shallower

water column. Thus, zones of convergent or divergent residual bedload transport can be

associated with shoaling or scouring areas, respectively. Equation (9) was used to

calculate tidally-averaged shoaling and scouring rates for the model domain.

2.4.3. Wetting and drying of intertidal areas.

Exposure times of different intertidal areas were calculated from the

model results and represented as a percentage of the tidal cycle. The exposure values

were superimposed on a tidal wetlands map to identify changes in exposure duration of

intertidal areas due to natural or anthropogenic (e.g. dredging-induced) causes.

2.5. Investigation of dredging scenarios.

Two proposed dredging scenarios were simulated by making changes in the

bathymetry of the harbor and by running the model with the same forcing constituents as

for the existing conditions. For each scenario, the subsequent analysis followed the

23

methodology used for the existing conditions, addressing effects of dredging on water

circulation, bedload transport, and intertidal inundation. The analysis included least

squares analysis of elevation, residual currents, exposure of intertidal areas, and

identification of scouring and shoaling patterns and rates in the harbor.

Suffolk County Department of Public Works presently attempts to maintain the

channels at a depth of approximately 1.8 m (6 ft) below MLW and a width of

approximately 30 m (100 ft) through occasional dredging. The first scenario involves

over-dredging of both Main Channel as well as Porpoise Channel to approximately 3.7 m

(12 ft) below MLW. This would provide underkeel clearance for relatively large boats

and could reduce the frequency of maintenance dredging. The width of the channels

would be kept at 30 m, but because of the deeper depth, a 5.5 m lateral increase on each

of the side slopes would be incorporated in the reconfiguration of the bottom topography.

This is due to a requirement for side slopes on navigation channels up to a maximum

slope of 1 on 3, to minimize slumping of channel edges [Suffolk County Planning

Department (1985)]. For a channel depth of 3.7 m (12 ft) below MLW, this translates to

approximately 11 m- (36 ft-) lateral-slope width from the channel to adjacent land

( MLW) on each side of the channel. This constraint was incorporated in the high

resolution of the altered grid.

The second dredging scenario investigated is illustrated in Figure 9. The

reconfiguration of the harbor was based on the first dredging scenario with one addition:

Over-dredging of the shallow end of the Main Channel south of the SBYC was also

included. This linked the two channels by creating a passage with a depth of 3.7 m (12 ft)

below MLW between south Young’s Island and north Horse Shoe Island. This resulted in

24

a bifurcating system of deep channels bordered by shallow intertidal regions. It was

estimated that the removal of the shallows in south Main Channel would double the

amount of sediment that would have to be removed compared to the first dredging

scenario. This translates to a total volume of 9.4x105 m3 of sediment removed by

dredging.

ADCIRC-2DDI was run on the altered bathymetries under neap and spring tide

forcing. West Meadow Creek was closed for spring tide runs because it had been found

that the predicted tides in WMC were poorly verified (see Table 9). The amount of water

entering the creek under the existing conditions (and under spring tides) was calculated to

be only 4.4% of the entire harbor’s tidal prism.

Each dredging scenario was then compared to the present case to produce a table

of quantifiable differences to be taken into account in the decision making process

concerning the viability of proposed dredging plans.

25

3. Results and discussion.

3.1. Tide measurements.

3.1.1. Tidal datums and low waters in HoH.

Gaps in the sea level record associated with the unavailability of

barometric pressure data were filled with data reconstructed from extracted tidal

constituents. On 09/14/00, a marked discontinuity in sea level of 1 m occurred after the

mooring of the SB tide gauge was apparently dragged by a passing boat to 275 m

southwest of that gauge’s deployment position (Table 2). The subsequent SB record was

corrected by adjusting its average sea level. Table 4 summarizes the estimated tidal

datums for SB and HoH with reference to MSL at each station based on a month’s data.

Tidegauge MHHW MLLW MLHW MHLW MHW MLW MTL MN

SB 1.06 m -1.06 m 1.05 m -1.04 m 1.06 m -1.05 m 0.01 m 2.11 mHoH 1.06 m -0.86 m 1.05 m -0.81 m 1.06 m -0.84 m 0.11 m 1.89 m

Explanation of symbols: Mean Higher High Water (MHHW); Mean Lower Low Water (MLLW); Mean Lower High Water (MLHW); Mean Higher Low Water (MHLW); Mean High Water (MHW); Mean Low Water (MLW); Mean Tide Level (MTL); Mean Range (MN).

Table 4. Tidal datums for Smithtown Bay (SB) and the head of the harbor (HoH).

Figure 10 shows the high and low water progression for the stations during

the first month of observations. High water elevations in SB and HoH were

approximately the same elevation for the period. A leveling survey showed that the

difference in MHW between SB and HoH is less than 2cm (Cademartori, 2001). High

26

water levels also appeared to be subject to the diurnal and fortnightly modulations present

in the tide (Figure 10). The low water level was set up at HoH compared to SB and was

relatively constant for the period, irrespective of the spring-to-neap variation in SB.

The constancy of the low water elevation at HoH suggests that harbor

morphology plays a major role in defining the MLW level. Stony Brook Harbor has an

average depth of approximately 0.9 m below MSL (Appendix A-2). Comparing this

number to the MLW in SB (Table 4), which is equal to 1.05 m below MSL, it becomes

clear that the bottom of the harbor on the average stands 15 cm above MLW in

Smithtown Bay. When the tide in SB approaches low water, part of the HoH basin is

deeper than the channels and has to drain through the two major channels (primarily

Porpoise Channel). The channels are at that time very narrow and shallow in certain

areas.

Increased friction in a shallow channel water column retards the ebbing of

the harbor to the point that HoH does not fully drain, never reaching the SB low water

level. Even when the tidal current turns in SB from ebb to flood, the harbor continues

ebbing. When the depth of water in SB becomes higher than the low water level in the

harbor a pressure gradient favoring flood develops and the harbor begins to fill. Tidal

asymmetry in the duration of flood and ebb, evident in the measured water elevations is

hence created in the harbor. This situation is more accentuated in WMC (Figure 11). The

head of the creek is deep and has to drain through a long, narrow, shallow channel

interspersed with shoals. Thus, the creek never completely drains prior to the tide rising

in SBH and refilling WMC.

27

3.1.2. Least squares harmonic analysis.

The tidal constituents extracted from the SB and HoH records are shown

in Table 5 along with harmonics from the NOAA primary station of Bridgeport, CT. The

results are consistent with the previous least-squares analysis of earlier data recovered

from approximately the same positions by Marcoe (1999). The major diurnal and

semidiurnal constituents at SB are comparable to their values at Bridgeport.

In general, the major equilibrium semidiurnal constituents (M2, S2 and N2)

considerably attenuate from SB to HoH (Table 5). Aubrey and Speer (1985) observed in

Nauset Inlet/Estuary, Cape Cod, MA the pattern of tidal dissipation, and found that

Nauset acts as a low pass filter, with larger amplitude decay rates for semidiurnal than

diurnal constituents. The zero-inertia model of Friedrichs and Madsen (1992), described

in §1.3, agreed with Aubrey and Speer (1985) hypothesis that the amplitude decay rate in

frictionally dominated embayments is proportional to frequency. At HoH, the attenuation

of the variance of the diurnal constituents K1, Q1, and O1 (~12%) is indeed much smaller

than that for the semidiurnal constituents M2, S2 and N2 (~30%). Similarly to Aubrey and

Speer (1985), diurnal components have shorter phase lags than semidiurnal ones.

28

Tidalconstituents

Bridgeport, CTSource: NOAA

Epoch data

SB08/15/00 1654 –09/27/00 1406

HoH08/15/00 1542 –09/27/00 1708

HoH – SB

Symbol Amplitudem

Amplitudem

Phaseº

Amplitudem

Phaseº

Attenuation%

Phaselag º

M2 0.985 1.016 344.5 0.858 7.5 16 % 23.0M4 0.012 0.015 248.0 0.168 312.8 64.8M6 0.014 0.008 313.5 0.024 282.7 329.1S2 0.166 0.180 356.5 0.124 26.3 31 % 29.8N2 0.215 0.210 173.5 0.132 194.2 37 % 20.7K1 0.091 0.083 87.4 0.069 102.1 17 % 14.7O1 0.066 0.047 204.1 0.057 227.9 -21 % 23.8S4 0.000 0.002 189.0 0.008 191.0 2.0N4 N/A 0.004 303.4 0.028 30.2 86.8L2 0.086 0.068 349.3 0.051 7.6 26 % 18.32N2 0.022 0.028 37.0 0.030 71.3 -7 % 34.3Q1 0.014 0.008 89.9 0.010 89.5 -32 % 359.6MSf 0.018 0.080 355.7 0.087 353.5 357.8

Symbol Frequencyrads/s

Name of tidal constituent

M2 1.4052x10-4 Principal lunar semidiurnalM4 2.8104x10-4 First M2 harmonic overtideM6 4.2156x10-4 Second M2 harmonic overtideS2 1.4544x10-4 Principal solar semidiurnalN2 1.3788x10-4 Larger lunar elliptic semidiurnalK1 7.2921x10-5 First lunisolar diurnal inequality constituentO1 6.7598x10-5 Second lunisolar diurnal inequality constituentS4 2.9089x10-4 First S2 harmonic overtideN4 2.7576x10-4 First N2 harmonic overtideL2 1.4316x10-4 Smaller lunar elliptic semidiurnal2N2 1.3524x10-4 Second order lunar elliptic semidiurnalQ1 6.4959x10-5 Larger lunar elliptic diurnalMSf 4.9250x10-6 Lunisolar synodic fortnightly constituent

Table 5. Tidal constituents (least-squares results) extracted from the observed marigrams in SB and HoH. Tidal epoch constituents from Bridgeport, CT, are included for comparison. Bridgeport is the primary NOS/NOAA tide recording station in the region.

The amplitudes of overtide constituents (M4, M6, S4, and N4) increase from

SB to HoH (Table 5). This is consistent with overtide production from their parent

constituents (M2, S2, and N2) through nonlinear processes. Overtide production in SBH

may mostly be associated with the increased friction in the harbor’s shallow interior as

explained by the zero-inertia model of Friedrichs and Madsen with a time-varying

29

diffusion coefficient (1992). According to that model, the second harmonic (first overtide

determining duration asymmetry) and the zeroth harmonic (which determines sea level

set up or down) are both governed by the parameters:

Lx / (relative distance from the head of the harbor, x, compared to the

length of the embayment, L),

Lk0 (with 10

−k scaling both the length of frictional dissipation and

the frictional length of the diffusive waveform), and,

γ [measuring the relative importance of time variations of channel

depth ( 0>γ ), versus time variations in embayment width

( 0<γ )]

For SBH, Lk0 1, and γ 0.62 (Friedrichs and Madsen, 1992). Since

0>γ , the shallow channel depth rather than the embayment width is the parameter

controlling the hydrodynamics in SBH. With 0>γ , the crest moves landward faster than

the trough (Friedrichs and Madsen, 1992). This causes a shorter-rising asymmetry inside

the embayment (flood-dominance) seen in the relative phase difference between the

principal semidiurnal component and its overtide, 2M°2 - M°4, (Speer and Aubrey, 1985).

Since the rate of decay of the waveform with distance is proportional to the square root of

0k , with 0>γ the amplitude of the crest decays more slowly than the trough, resulting in

sea level set up (Friedrichs and Madsen, 1992). Finally, for 0>γ and Lk0 =1, the high

water levels along the harbor’s channels are predicted by the zero-inertia model to be

leveled, as was observed in SBH.

30

The short length of the record limited the number of constituents resolved

by least-squares analysis of sea level from WMC (Table 6). Due to greater L (and thus

lower Lx / and higher Lk0 ), the effective distance over which the signal travels from

SB increases. Thus, M2 decreases to 0.729 m in WMC, compared to 0.858 m in HoH and

1.016 m in SB. The M4 overtide production is marked as well, reaching 0.177 m,

compared to 0.168 m in HoH and 0.015 m in SB. The diurnal constituent K1 attenuates

even more in WMC (0.059 m) than in HoH (0.069 m), compared to SB (0.091 m).

Table 6 includes results from the Stony Brook Yacht Club (SBYC) tide

gauge based on data taken earlier in the year 2000. These results should be interpreted

with caution due to the high probability of a tide gauge malfunction (Appendix A-1).

Tidalconstituents

WMC08/15/00 1654 – 08/22/00 2118

SBYC03/03/00 1548 – 04/14/00 1538

Symbol Amplitude, m Phase, º Amplitude, m Phase, ºM2 0.729 17.5 0.878 180.0M4 0.177 355.1 0.040 311.8M6 0.024 277.8 0.042 187.4K1 0.059 105.4 0.068 188.3

For explanation of tidal constituent symbols see Table 5.Note: According to the Rayleigh bandwidth criterion, only the presented limited information can be extracted from the short period of observations in WMC (8 days).

Table 6. Tidal constituents (least-squares results) extracted from the observed marigrams in WMC and SBYC. Results from SBYC should be interpreted with caution (see Appendix A-1).

31

3.1.3. Implications for flood dominance.

A measure of the intensity of the flood-dominant asymmetry in a shallow,

friction-dominated, semidiurnal tidal environment like SBH is the ratio a/h between the

offshore M2 tidal amplitude and the average depth of the channels (Friedrichs and

Aubrey, 1988). The area of the channels at MLW in SBH is 1.74x106 m2, and the volume

of water they can contain if filled to MSL is approximately 3.26x106 m3. Thus, the

average channel depth, h, is 1.87 m relative to MSL. The offshore tidal amplitude a (for

M2) in SB is 1.02 m (Table 5). Then, the a/h ratio for Stony Brook Harbor is 0.54

[compare to 0.55 by Marcoe, (1999)].

According to Speer and Aubrey (1985), such a high a/h ratio is

characteristic of flood-dominant systems. Maximum duration asymmetry in the rise and

fall of the tide favoring longer ebb is expected when the relative phase between the

semidiurnal constituent M2 and its major overtide M4 (2M°2 - M°4) is 90° (Marcoe, 1999).

On the other hand, if the relative phase is 270°, floods are longer than ebbs. The 2 -

M°4 relative phase is 63.6° at HoH and 39.9° at WMC, favoring longer ebb duration and

thus higher flood than ebb currents (Tables 5-6). The magnitude of this flood-dominant

asymmetry can be measured by the relative overtide production as seen in the M4/M2

amplitude ratio, which is 0.20 at HoH and 0.24 at WMC.

3.1.4. Fortnightly variation in sea level asymmetry.

One important characteristic of the tide in SBH is the fortnightly

modulation in semidiurnal tides present in SB as well as inside the harbor. To simulate

the extremes in tide range variability and design the model runs, two 48-hr periods were

32

selected for least squares analysis: spring tide conditions 08/30/00-08/31/00 and neap tide

conditions 09/07/00-09/08/00 (Figure 12).

Least squares results of the two selected neap and spring tide periods for

SB and HoH are shown in Table 7. From neap to spring, the equilibrium semidiurnal tide

M2 grew in amplitude by 65% in SB from 0.79 m to 1.30 m. This increase in tidal range

from neaps to springs caused an increase in the tidal prism, which, in turn, increased the

magnitude of the tidal currents inside SBH. Faster currents accentuated the importance of

quadratic friction in generating the M4 overtide. Thus, the overtide growth ratio between

M4 and M2 at HoH increased to 0.24 at spring tides from 0.16 at neaps [compare to 0.231

and 0.167, respectively; Marcoe (1999)] indicating greater potential for asymmetry

during spring tides.

HoH-SB(Neaps – springs)SB

(Neaps – springs)HoH

(Neaps – springs) Attenuation(%)

Phase lag(º)

M2 (m) 0.786 – 1.304 0.690 – 1.021 12% – 22% 29.1 – 32.3 M4 (m) 0.004 – 0.035 0.112 – 0.244 98.5 – 87.8

M4/M2 0.01 – 0.03 0.16 – 0.24 2M°2 - M°4 101.4 º – 79.9 º 61.1 º – 56.5 º

SB 0.135 Increase in average sea level (m) from neap to spring tides: HoH 0.216

Table 7. Neap to spring tide variation in M2, M4, and tidal asymmetry.

33

3.2. Hydrodynamic model evaluation.

In the following sections (§3.3-3.7), model results including sea level and current

predictions are presented. The procedure used to quantitatively evaluate the performance

of the model is based upon computing the mean absolute error, MAE, the root mean

square error, RMSE, and the relative average error based on variance,

E=1-d2 (10)

where d2 is the index of agreement [Blumberg and Goodrich, (1990), and Willmott et al.

(1985)]. For SB, HoH, SBYC, and WMC, the MAE and RMSE are given in Table 8 in

units of cm, along with the relative average error in percentile form (E=0% means null

difference between model and observations).

In WMC, spring tides were not adequately described by the model (Table 8).

West Meadow Creek – and especially Aunt Amy’s Creek perhaps contains

insufficiently resolved areas due to the Creek’s shallowness, steep localized bathymetric

gradients, and narrowness of its channel compared to the highly dissipated marshy areas

that surround it. Therefore, model results from WMC under spring tide conditions are of

poor quality and will not be presented.

The average index of agreement (d2) for sea level under neap tides is 99.3%. For

spring tides (excluding WMC) the average d2 is equal to 99.4%. The average model

accuracy in sea level predictions based on RMSE is 6 cm for neap tide simulations and 9

cm for spring tides (excluding WMC).

34

Sea level (all modeled constituents).Neap tides MAE (cm) RMSE (cm) E (%)SB <0.1 <0.1 0.0%HoH 4.3 4.9 0.3%SBYC 5.0 5.6 0.4%WMC 10.6 12.5 2.0%Spring tidesSB 0.4 0.4 0.0%HoH 10.7 13.8 1.0%SBYC 10.9 13.0 0.9%WMC 34.7 38.7 27.4%

M2Neap tidesSB <0.1 <0.1 0.0%HoH 3.6 4.0 0.2%SBYC 0.0 0.0 0.0%WMC 9.1 10.1 1.4%Spring tidesSB 0.4 0.4 0.0%HoH 7.7 8.6 0.4%SBYC 9.2 10.2 0.5%WMC 34.6 38.5 29.7%

M4Neap tidesSB 0.0 0.0 0.0%HoH 0.8 0.9 0.3%SBYC 1.7 1.8 6.8%WMC 6.6 7.3 13.2%Spring tidesSB 0.0 0.0 0.0%HoH 1.5 1.6 0.2%SBYC 7.1 7.9 24.1%WMC 3.1 3.5 2.6%

DiurnalNeap tidesSB 0.0 0.0 0.0%HoH 1.0 1.2 0.7%SBYC 4.8 5.3 9.2%WMC 1.2 1.3 1.0%Spring tidesSB 0.0 0.0 0.0%HoH 0.4 0.4 0.6%SBYC 1.1 1.2 8.9%WMC 2.5 2.8 25.0%

Table 8. SBH model: Skill assessment.

35

3.3. Model results: Tidal hydrodynamics.

3.3.1. Sea level.

3.3.1.1 Time series.

Figures 13-14 illustrate model results for sea level at selected stations

from the two channels in SBH under both spring and neap tide forcing. Two semidiurnal

periods are presented to show the diurnal modulation. Comparison of Figures 13-14

reveals that for both Porpoise Channel (PC) and Main Channel (MC), high waters along

these channels reach approximately the same elevation. On the other hand, low waters

rise from SB to HoH. This rise is mostly evident at the outer channel and not inside the

embayment.

The tidal range in SB increases from 1.56±0.13 m during neap tides to

2.62±0.07 m during springs. These numbers correlate well with Marcoe’s (1999) estimate

of mean tidal range of 2.13 m at SB. The considerable increase in tidal range (1.06±0.20

m) has an equal effect on high and low water elevations at SB: high waters become

higher, while low waters become lower approximately by the same amount (Figures 13-

14).

Inside the harbor, however, neap to spring changes in the high water

level are greater than the neap to spring changes in the low water level. For harbor

stations inside from the inlet mouth (station I2, Figure 5), low water elevations during

spring tides were only 3±1 cm lower than during neap tides. Compare this number with

the SB station where the low water level dropped more than 50 cm from neap to spring

tides.

36

This constancy in low water levels inside the harbor between neap and

spring tides is also seen in the observed data (Figure 10). The increased tidal range during

spring tides involves a large increase in the volume of water contained in the harbor at

high tide relative to the high water volume during neaps. However, the difference

between the volume of water that can be stored in the harbor at low water between neaps

and springs is relatively small (Dyer, 1986). These results show that low water elevations

inside SBH are relatively constant and independent of the neap to spring variation in

boundary forcing.

3.3.1.2.Harmonic analysis.

Figures 15-20 show results from least squares harmonic analysis for

stations distributed along the three longitudinal transects. The most rapid reduction in

amplitude of the principal semidiurnal constituent, M2, takes place in the inlet (Figure

15). M2 attenuation is higher at the inlet during springs than during neaps, most likely

because of increased velocities that accentuate the magnitude of quadratic friction. South

of the southern end of the two major channels, the amplitude of M2 is approximately

constant: 0.91 m at spring tides and 0.64 m at neap tides.

The phase of M2 is shown in Figure 16. The phase lag between SB and

HoH3 (Figure 5) is approximately 30° irrespective of the tidal forcing. Under neap tides,

the longest M2 phase lag is seen in WMC (being almost a constant 50° north of Aunt

37

M4 creation occurs primarily in the inlet (Figure 17). However, under

springs, but most importantly under neap tides, M4 is also created from shallow water

processes in the channels inside from the SBH mouth (PC1-5 and MC1-5 stations).

The landward attenuation of M2 and the production of M4 are

associated with the rise in low water level. This, in turn, is associated with a landward

increase of the zero frequency sea level constituent, Z0, from 0 cm in SB to 6 cm (neaps)

or 22 cm (springs) at the head of the harbor (Figure 18). A dynamic argument by

Robinson et al. (1983) indicates that this set-up in Z0 within basins like SBH is primarily

caused by the ebb to flood asymmetry in bottom stress.

The increased tidal asymmetry during spring tides can be seen in the

relative overtide growth (Figure 19). The M4/M2 ratio increases inwards from the inlet

due to both the attenuation of M2 and the creation of M4. At HoH, the ratio is higher

during spring tide forcing (0.27 compared to 0.16 during neaps). The neap to spring

increase in M4/M2 by 69%, and the decrease in 2Mº2 - Mº4 by 11% (Figure 20) are

consistent with the results of complex demodulation performed by Marcoe (1999) for

observations taken from HoH.

The largely flood-dominant behavior of SBH is seen in the relative

phase difference 2Mº2 - Mº4 (Figure 20): Inside from Young’s Island, 2 - M°4 ranges

between 37º-48º indicating flood-dominance. However, there is considerable variability

in 2Mº2 - Mº4 at the channel entrances under neap and spring tide forcing. At the

beginning of the channels, under neap tides, minima develop in the relative phase curve

(Figure 20), due to local maxima in the phase of M4. These minima in 2M°2 - M°4 are

accentuated at the vicinity of Jen’s Island (point of intersection of the three main

38

flowways, Figure 1). There, the relative phase becomes close to 0º during neap tides,

resulting in a positive symmetric tide. Positive symmetric tide here is defined as in

Friedrichs and Aubrey (1988): nearly stationary sea level symmetric about low waters,

associated with increased friction at low waters and 2M°2 - M°4 = 0º (as opposed to

negative symmetric tide about high waters with 2M°2 - M°4 = 180º). Presence of a

symmetric tide implies no net accumulation or removal of bedload sediment during neap

tides.

3.3.2. Transient velocity.

3.3.2.1. Polar plots.

Polar plots of velocity time series at certain model stations (Figures

21-24) indicate the importance of advective accelerations in SBH and the general pattern

of higher maximum flood than ebb currents.

Figure 21 shows that the tidal current in the deep waters of Smithtown

Bay (2,000 m northeast of station SB) is a slow (<6 cm/s) rotary one (with clockwise

rotation). In the inlet (station I2; Figures 21 and 5) the current becomes rectilinear, and as

fast as 1.27 m/s. The change in direction between ebbing and flooding currents in the

inlet is not 180º. This result shows the importance of advective accelerations inside the

inlet mouth as previously hypothesized by Marcoe (1999) because sea level gradient

forcing cannot produce such bathymetric steering.

Main Channel and PC stations (Figures 22-23) also show the

importance of nonlinear accelerations. For example, current magnitudes are higher in PC

than in MC, and thus their inertia keeps them streamlined compared to the more scattered

39

flow in MC. The asymmetry in maximum flood to ebb currents inside the channels

increases moving toward the head of the harbor. At HoH (Figure 24), velocities drop

considerably, and the flow is influenced by an increased zero frequency (residual or

mean) component. Velocities from two stations in WMC (WMC4 and WMC6) were

flood dominant as well, but of noticeably lower speeds than in the two other channels

(<15 cm/s under neap tides).

3.3.2.2. Description of the circulation in SBH.

When the water level reaches LW at the HoH exposing Horse Shoe

Island (Figure 1), SB has already started flooding and the rising sea level has completely

inundated the ebb shoal. About 2 hrs later, maximum flood current occurs at the inlet

mouth. The greatest velocities predicted by the model are 1.49 m/s for neap tides, and

2.03 m/s for springs. Maximum bay-wide velocities occur on a flood tide inside the inlet,

at the region of abrupt decrease in depth (Figure 6), as water exits the inlet’s deepest

scoured point to enter the shallows north of Young’s Island. These values are comparable

with other research previously conducted in SBH (see Chapter 1). Six hours after low

waters at SB, but only 4 hrs after low waters at HoH, high waters occur in SB, signaling

the beginning of the ebb cycle.

Only 30 min (for springs) to one hour (for neaps) later, high waters

reach HoH, ending a flood cycle that has lasted less than 5 hrs there. After high waters

reach HoH, the head of the harbor basin starts ebbing. Ebb there lasts 7.5 hrs. Ebbing

velocities are weaker than during the shorter flood and the harbor never completely

drains. The large pressure head that develops across the restricted inlet produces the ebb

40

jet in SB: at the moment of maximum pressure head across the inlet (during ebb at spring

tides), sea level at the inlet station I2 can be as much as 71 cm higher than sea level at

station SB (Figure 25).

3.3.2.3. Harmonic analysis.

The least-squares harmonic analysis of velocity time series taken from

the model output for selected model stations shows the character of the tidal asymmetry

in the currents. The relative overtide growth associated with depth-averaged velocity

along a station’s major axis, uM4/uM2, can be as high as 0.51, at station HoH1 during

spring tides (Figures 26-27). Clearly flood-dominant currents are formed at the stations at

the southern end of the two major channels and at HoH. Station PC4 (Figure 5), for

example, has a relative phase difference in velocity (2uMº2 - uMº4) equal to 16.7º and

9.10− º under neap and spring tides, respectively. For tidal velocities, a relative phase of

-dominant behavior (Aubrey and Speer, 1985). At station PC5

(Figure 5), 2uMº2 - uMº4 is equal to 33.7º and 9.4º for neaps and springs, respectively.

Relative phase at HoH stations ranges between –19.4º at station HoH3 (Figure 5) under

spring tides, and 44.2º at station HoH1 (Figure 5) under neap tides.

3.3.3. Eulerian residual currents.

3.3.3.1. Residual currents.

The computed Eulerian residual currents are shown in Figure 28 for

spring tides. For neaps, the magnitude of the residual currents drops by 25-50%. The

residual currents are not zero in the harbor entrance but rather are directed seaward. The

41

associated flux is balanced by an inward Stokes transport due to the partially progressive

character of the tidal wave. Thus, the residual water transport across the inlet is

approximately zero indicating that no significant amount of water is on-the-average

moving in or out of the harbor. The Eulerian residual currents in Figure 28 are consistent

with findings from Lagrangian drift-card surveys conducted by Bowman (1988). These

surveys showed the tendency of the majority of the cards to be flushed out of SBH,

unless they had been released at the extreme back of the bay.

The fact that the harbor does not have a tidally averaged tendency to

fill or empty is better illustrated in Figure 29 for tidal cycles of the greatest simulated

forcing period (diurnal). The water volume curve for every other semidiurnal tidal period

is practically repeating itself when each figure is regarded separately. Again, the volume

of water stored inside SBH at low waters is almost constant (~2.6x106 m3) and does not

depend upon the spring to neap or diurnal changes in tidal forcing. It is obvious that the

harbor – inside from its mouth – does not feel the sea level gradient force when SB is

close to low water.

The tidal prism increases significantly (by about 67%) from neap to

spring tides. This greater spring-tide volume is transported into the harbor in less time

than during neaps (Figure 29), resulting in higher asymmetry in the currents during

springs.

3.3.3.2. Residual depth-averaged vorticity.

An analysis of the depth-averaged vorticity can help to explain the

formation of the residual eddies inside SBH (Figure 28). The two-dimensional

42

momentum equations can be combined through cross-differentiation to form the one-

dimensional equation (11):

{

( ) 0=⎟⎟⎠

⎞⎜⎜⎝

⎛×∇−⎟⎟

⎠

⎞⎜⎜⎝

⎛×∇+

+−∇•+

43421

vv

4434421

vv

44 344 21321vv

DiffusionVorticity

HE

Friction

Huu

C

StretchingVortex

dtdH

Hf

AdvectionVorticity

u

yofVorticitonAccelerati

Localt

DD

ωω∂ω∂ (11)

where ω is the vorticity based on depth-averaged velocity, defined as:

ω ∂∂

∂∂

≡ −vx

uy

, (12)

and positive counterclockwise, while vED is the lateral eddy diffusion in the x and y

dimensions.

The frictional term in equation (11) can be further expanded to three

terms: vorticity dissipation through friction, frictional torque due to velocity shear, and

frictional torque due to depth gradient (Park, 1990). Then, equation (11) states that the

transient vorticity is a) generated through water column stretching or squeezing, the

frictional velocity shear, and the frictional depth gradient, and b) dissipated by frictional

resistance and lateral diffusion.

In order to investigate the creation of the residual gyres at HoH, four

stations where chosen (V1 through V4) and are shown in Figure 30 superimposed on

bathymetric contours and the residual depth-averaged velocity field for easy reference.

These stations were around a depression at HoH.

Table 9 shows the results of the vorticity balance analysis conducted

for the stations of Figure 30. The different terms of equation (11) were evaluated and then

43

averaged over two semidiurnal tidal cycles. For the stations positioned close to the

intense counter-rotating gyres at HoH (stations V1 and V2), the vortices are primarily

created by vortex stretching due to topographic rectification (term b, Table 9). At the

more distant station V3 vorticity advection becomes important (term a, Table 9).

Simulation Neap tides Spring tidesStation V1 V2 V3 V4 V1 V2 V3 V4Depth, m 2.75 2.06 2.41 1.91 2.75 2.06 2.41 1.91Residualvorticity, Hz 5.7x10-4 -2.7x10-4 2.0x10-4 5.7x10-4 6.8x10-4 -2.7x10-4 3.3x10-4 7.2x10-4

a. Vorticity advection,10-12 Hz2

-18,020 64,930 -15,800 336,900 21,380 -23,290 -53,890 702,500

b. Vortex stretching,10-12 Hz2

-30,830 153,100 2,744 -546,500 -61,990 269,200 3,380 -862,800

c. Friction,10-12 Hz2 46,440 -77,180 11,600 174,800 76,720 -141,000 28,440 290,100

d. Vorticityeddydiffusion,10-12 Hz2

2,410 -140.850 1,456 34,800 -36,110 -104,910 22,070 -129,800

Table 9. Residual vorticity analysis (depth-averaged vorticity balance) at HoH vorticity stations V1-4.

Station V4, with its high vorticity advection term manifests the

advection of vorticity at the end of a flood-dominant channel, as the tidal race developed

during flood in the channel intensely empties to the slower-moving back-basin. The

presence of the depression at the back of the channel (Figure 30) creates then a cyclonic

(positive, or counterclockwise) vorticity through vortex stretching, that is not averaged-

out during the slower and shallower ebb that follows (station V1). Vortex squeezing on

the other hand, which happens in the south, west, and east fringes of the depression,

creates anticyclonic motion. In station V2, this motion is more intense than elsewhere due

44

to that station’s proximity to the higher bathymetric gradient of the deeper part of the

depression.

3.4. Model results: bedload transport.

Results for the instantaneous and residual bedload transport patterns for the

existing configuration of SBH are presented in this section. Transient and residual

bedload transport along with spatial patterns of shoaling and scouring associated with

residual bedload divergence are discussed. In subsequent sections (§3.6) these results are

compared to the bedload patterns after the bathymetry of the harbor is modified to

simulate dredging scenarios.

3.4.1. Transient and residual bedload transport patterns.

The ratio of flood-directed to ebb-directed bedload transport was

calculated across the inlet, northern PC, and northern MC. The results indicate that there

is a net influx of bedload through the inlet from SB. Because of the very high threshold

shear stress required to mobilize the inlet gravel, no motion is achieved there during the

first experiment (Table 10). Maximum currents almost everywhere inside SBH are

directed inwards. Thus, the residual bedload transport is flood-dominant within the

channels (Figures 31-32). The patterns intensify during spring tides but are nowhere

reversed. These results are similar to those of Aldridge (1997) for Morecambe Bay, U.K.

45

Transect NumericalExperiment

Floodtransport,

m3

Ebbtransport,

m3

Net inward transport,

m3

Flood toebb ratio

First 0.0 – 0.0 0.0 – 0.0 0.0 – 0.0 N/D – N/DInlet Second 14.6 – 60.9 8.0 – 42.9 6.5 – 18.0 1.8 – 1.4 First 11.7 – 57.5 2.2 – 7.9 9.6 – 49.5 5.4 – 7.2 PC Second 20.2 – 70.9 8.8 – 18.1 11.4 – 52.8 2.3 – 3.9 First 0.0 – 1.5 0.0 – 0.4 0.0 – 1.1 N/D – 3.7 MCSecond 0.5 – 3.7 0.3 – 1.9 0.1 – 1.8 1.4 – 2.0

Flood to ebb ratio higher than unity indicates flood-dominant transport.N/D: Not defined (zero transport).First numerical experiment: based on varying sediment types according to sediment map.Second numerical experiment: based on spatially uniform sandy bottom.Ranges shown are from neaps to spring tides (neaps – springs).

Table 10. Tidal characteristic number of bedload transport: flood to ebb ratio.

3.4.2. Residual bedload transport divergence.

Residual bedload transport divergence results are presented in Figures 33

and 34-34a for the case of non-uniform sediment types (first numerical experiment), and

in Figures 35 and 36 for the case of spatially uniform sand (second numerical

experiment). Bed accretion rates for particular model station sites are shown in Figure 37

in units of mm/day. Figures 33-36 show that bed change patterns alternate between

accumulating and eroding areas. These patterns are in general coherent due to the very

high resolution of the computational mesh. Divergence calculations, however, are

sensitive to the grid size and patchiness may, in part, depend on the size of the finite

elements.

Scouring and shoaling patterns are very similar in each experiment

between neap and spring tides. Under spring tides however, the patterns spread, and bed

46

changes intensify due to higher currents. At the head of the harbor, bedload transport is

not detected for any forcing or experiment. Bedload transport divergence is zero in outer

SB, a result consistent with Signell et al. (2000). Areas of residual divergence and

convergence are mostly confined in the channels. Porpoise Channel in particular is a

convergent (shoaling) area. On the other hand, the intertidal shoals and vegetated regions

are low energy environments unable to support bedload transport. It is likely that

suspended rather than bedload sediment transport is the most important in marshy areas

(Dyer, 1986).

Inside SBH, for the existing sediment distribution, northern PC and the

area north of Young’s Island are predicted to shoal most rapidly. Some parts of MC also

accumulate sediment. Processes not included in the model, such as undercutting of the

Young’s Island dredged material may be of importance in MC. Historic evidence

indicates that the elevation of Young’s Island dredged material has decreased since its

creation (Robbins, 1977). This may be associated with erosion and collapse of the spoil’s

fringes (Robbins, 1977), although compaction of this material cannot be ruled out. For a

short description of the undercutting mechanisms and its effects on bank stability see

Fagherazzi and Furbish (2001). The region of the Stony Brook Boat Works appears to be

shoaling as well, especially during spring tides (Figure 34a).

The inlet floor appears to be stable, but the ebb-dominated outer channel

has a tendency to erode (Figures 33-34). The figures indicate that some of the sediment

exported out of the inlet during ebb is deposited in a bar attached to West Meadow

Beach. However, the spatial distribution of shoaling areas in the outer inlet, away from

47

the tide-dominated mouth, can be severely affected by longshore transport processes not

included in the present analysis (Komar, 1996, Hayes, 1975).

The second numerical experiment indicates that the channel in SB lies

between an eroding area to the west and the shoaling bar to the east (Figure 36). The

channel is thus dynamically stable following a storm. For the second numerical

experiment, new areas of shoaling appear inside the inlet.

3.5. Model results: Inundation map of tidal flats.

Figure 38 shows mean daily exposure (drying) of intertidal areas in hrs/day for

both neap and spring tides. This figure is used to assess flooding of the marshes in SBH

under the present conditions and to provide a means for comparison – in later chapters –

with alterations induced by dredging. Positions of marshes according to the NYSDEC

Tidal Wetlands maps (1974) are delineated. Barren intertidal regions are shown as well.

Salt water flooding of a canopy for 2 hrs by one percent of the high waters during a year

affects vegetation (Redfield, 1972). This translates to only 7 high waters, or 14 hrs of

salt-water inundation per year.

Because the low water levels inside the harbor are approximately equal between

neap and spring tides, inundation differences at low waters inside the harbor between

neap and spring tides are small (Figure 38). Outside the inlet mouth however, neap to

spring changes in the temporal and spatial variation of wetting-and-drying regions

become more visible.

Figure 38 shows differences between the position of the marshes based on the

Tidal Wetland maps (NYSDEC, 1974) and the wetting and drying regions predicted by

48

the model. Some areas that appear vegetated (and hence intertidal) on the NYSDEC tidal

wetland maps appear to be subtidal (dark blue) in Figure 38, and vice versa. It is

interesting that, based on this observation, Young’s Island and its marshes could be

shrinking, while the marshland of Horse Shoe Island may be migrating and spreading to

the south (possibly due to the flood-dominant behavior of the harbor). Such comparisons

are difficult, since not all of the intertidal areas in the embayment are currently vegetated.

3.6. Evaluation of response to dredging both channels to 3.7m (12ft) below

MLW (first dredging scenario).

Model results presented in this and the next sections are used to address the fourth

objective of this study. Namely, the evaluation of dredging-induced changes in the

existing state of tidal hydrodynamics, bedload transport, and inundation of intertidal areas

in SBH as these were predicted by the model’s simulation of the two proposed dredging

scenarios.

3.6.1. First dredging scenario: Tidal hydrodynamics.

Comparison of the sea level time series in Figures 39-41 (first dredging

scenario) with Figures 13-14 (existing conditions) reveals that considerable changes

would occur after dredging. Low waters throughout the harbor (except in WMC) will be

lower by 2.5-8.5 cm (neap-spring tides). During neap tides, the duration of ebb will

decrease: thus, the duration of ebb will be only 1.24 hrs greater than the duration of flood

for both neap and spring tides. This is associated with a decrease in the á/h ratio (or,

49

equivalently, the decrease in parameter ã) and the resulting reduction in bottom friction

from the deepening of the channels.

Under the existing conditions, a localized truncation of the sea level curve

was present in the vicinity of the shallow station MC3 (Figure 5), evident in the very high

LW elevations there (Figure 14). Dredging of MC to 3.7 m (12 ft) below MLW, removed

this behavior by making the sea level time series of stations MC1 and MC3 (Figure 5)

almost indistinguishable (Figures 40 and 14). WMC, on the other hand, appears to be

relatively less affected by the dredging of the channels in the harbor (Figure 41).

Channel deepening leads to a decrease in the contribution of bottom

friction to the momentum balance. Thus, the attenuation of the primary semidiurnal tidal

constituent inside the harbor is reduced after the implementation of the first dredging

scenario for both neap and spring tides (Figures 42 and 15). The M2 phase retardation is

also reduced at the Main and Porpoise Channels (Figures 43 and 16). Changes in WMC

appear to be minimal.

Increased channel depths reduce the quarter-diurnal overtide (Figures 44

and 17). However, in WMC, M4 production increases due to a small increase in the tidal

prism and the M2 amplitude at the mouth of the creek. The M4 phase also changes after

dredging. The maxima in M4 phase seen in the channels under the existing conditions,

which in turn cause minima in 2M°2 - M°4, persist after dredging. The persistence of the

M4 phase peaks in the beginning of the two main waterways may perhaps be associated

with a localized increase of nonlinear advective accelerations due to increase in the

amplitude of M2.

50

Figure 45 shows that the set-up in MSL (Z0 constituent) is greatly reduced

after dredging except in WMC. In a frictionally dominated environment like SBH, sea

level set-up is primarily caused by asymmetric friction between flood and ebb [Robinson

et al. (1983)]. For the first 58 tidal cycles contained in the HoH tide gauge record, the

monthly-average mean depth during flood, fH , is 6±9 cm greater than the depth during

ebb, eH . Since eH < fH , the depth-averaged bottom friction is stronger during ebb. This

leads to tidally-averaged friction directed towards flood that is balanced by a tidally-

averaged surface slope (sea level set-up). Significantly deeper bathymetric channel depth

(h) after dredging, decreases the relative importance of sea level tidal fluctuations (ç) in

determining the total water column depth (H=h+ ç); this in turn reduces the differences

in bottom friction felt in low versus high waters. The decrease in asymmetric friction

after dredging leads to the decrease in sea level set-up (Figure 45).

Dredging reduces the magnitude of tidal asymmetry in SBH. The relative

overtide growth ratio, M4/M2, is reduced to 75%-80% of its pre-dredging value at HoH

(Figures 46 and 28). This decrease in the magnitude of tidal asymmetry is not

accompanied by a considerable change in 2M°2 - M°4, so that, after dredging, the harbor

remains flood-dominant (Figures 47 and 29).

The currents in the channels decelerate after over-dredging (Figures 48-49

and 22-23), due to the local increase in the channel cross-section. On the other hand, non-

dredged stations show that currents accelerate there; this may primarily be associated

with less frictional dissipation in the dredged channels and with an increase in the tidal

prism (Figures 50-51, and 21, 24).

51

Figure 52 shows the differences in residual currents between the first

dredging scenario and the existing conditions. After dredging, Eulerian residual vectors

inside SBH remain largely ebb-directed and intensify, especially at the back of the

harbor. Thus, exchange of the waters in that region is expected to be more efficient after

dredging.

3.6.2. First dredging scenario: Bedload transport.

Net transport increases only at the inlet after dredging. At the inlet mouth,

higher velocities double the magnitude of bedload transport when a spatially uniform

sandy bottom is considered (second numerical experiment, Tables 11 and 10). Assuming

that after dredging the sediment map of SBH will not change considerably (first

numerical experiment), higher velocities will still not be sufficient to move the gravelly

inlet bottom. Inside SBH however, bedload transport will decrease after dredging, due to

the lower velocities in the deeper channels. For the dredged MC transect, sand-bed

motion is measurable only under spring tides, and even then, it is very small compared to

the existing conditions.

It is not only the magnitude of the instantaneous bedload transport that

will be reduced in the dredged channels; the residual bedload will decrease as well, both

in magnitude and area (Figures 53-54 and 31-32) because of the decrease in tidal

asymmetry inside SBH after dredging.

52


Floodtransport,

m3

Ebbtransport,

m3


m3

Flood to ebb ratio

First 0.0 – 0.0 0.0 – 0.0 0.0 – 0.0 N/D – N/DInlet Second 17.3 – 78.9 10.1 – 39.2 7.2 – 39.7 1.7 – 2.0 First 2.4 – 25.0 0.1 – 2.8 2.3 – 22.1 20.8 – 8.8 PC Second 7.2 – 35.4 2.7 – 9.0 4.5 – 26.5 2.7 – 4.0 First 0.0 – 0.0 0.0 – 0.0 0.0 – 0.0 N/D – N/DMCSecond 0.0 – 0.7 0.0 – 0.1 0.0 – 0.6 N/D – 5.0


Table 11. Tidal characteristic number of bedload transport: flood to ebb ratio.First dredging scenario. For comparison to Table 10 (existing conditions).

The residual bedload divergence (scouring) and convergence (shoaling)

Figures 55-58 (and Figures 33-36) show the reduction of shoaling rates and shoaling

areas inside SBH after dredging. In SB, shoaling rates and spatial distribution of shoaling

areas seem relatively unaffected by dredging. Figure 59 (as compared to Figure 37;

existing conditions), shows the general reduction in shoaling rates after dredging that

takes place in almost all model stations with the exception of one: higher shoaling rates

are predicted for the inlet-mouth station I2 if a uniform sandy bottom is considered

(Figure 59).

After the implementation of the first dredging scenario, the entire domain

will experience a reduction in the volume of bedload sediment expected to accrete

because of tidal processes. In the next section (§3.7), a calculation of the volume

deposited per year in shoaling areas is carried out. That calculation shows that the

53

sediment volume deposited annually through tidal processes in areas with predicted

shoaling rates greater than 0.1 mm/day will decrease to about 69% of its existing value

for the entire domain, and to only 42% of its existing value inside from the inlet mouth.

3.6.3. First dredging scenario: Inundation changes in intertidal areas.

The Suffolk County Planning Department (1985) recommends limiting

“maximum changes, due to navigation channel dredging, of water levels at the heads of

embayments at MLW and MLW to 0.076 m (3 inches), or 5 % of the mean tidal range,

whichever is less” in order to avoid “changes in salinity, exposure of mudflats, drowning

of low-lying lands, etc.” Five percent of the mean tidal range in SBH is about 0.10 m.

The elevation of average LW is expected to fall about 0.058±0.029 m under spring tide

forcing (0.029±0.002 m under neap tides) at HoH and depending on the diurnal

constituent. If the usual up-to-61-cm (2 ft) over-depth will be allowed for dredging, the

further decrease in asymmetry and sea level set up (due to decrease in a/h) may lower

LW at HoH even more. For WMC, under the simulated neap tide forcing, the average

LW level is expected to change much less (see Figures 41 and 17).

The average daily exposure of intertidal flats and marshes will increase

after dredging by 1.07-1.77 hrs (neap to spring tides) as the low water level drops inside

the harbor. This increase in drying will be even higher than 4 hrs/day in some areas

(Figure 60).

54

3.7. Evaluation of response to dredging both channels to 3.7 m and expanding

MC (second dredging scenario).

3.7.1. Second dredging scenario: Tidal hydrodynamics.

The sea level curves for selected model stations along the three

conveyance channel lines (Figures 61-62) show that the high water elevation will remain

approximately the same, that the high water lag between SB and HoH will decrease, that

low water levels will drop inside the harbor, and that the tide will become less

asymmetric. However, as in the previous simulations, low water levels inside the harbor

will not vary much between neap and spring tides.

The M2 will attenuate less under the second over-dredging scenario than

under the existing conditions by an amount similar to the first scenario. The predicted

changes in M4 are about the same as in the first dredging scenario: namely, less overtide

production after dredging, due to less friction. The above results and their implications on

tidal asymmetry after the implementation of the second dredging scenario are

summarized by the parameters M4/M2 and 2Mº2 - Mº4 (Figures 63-64, and 46-47, 19-20).

The tide will become less intensely flood-dominant after the second dredging scenario in

comparison to the existing conditions due to the reduction of friction: M4/M2 at HoH will

decrease by 18-23%. The difference between the neap to spring asymmetric behavior

(2Mº2 - Mº4) inside the channel entrances, will decrease from 20-30º to approximately 5º.

Currents in SB, at the inlet mouth (I2), and at HoH (HoH1 and HoH3) are

predicted to change only slightly before and after the removal of the shallows. However,

MC and PC stations (Figures 65-66 and 48-49) reveal that currents in MC increase, while

55

those in PC decrease. This is probably due to a higher percentage of the tidal prism

conveyed through the now less restricted MC.

3.7.2. Second dredging scenario: Bedload transport.

The magnitude of transient bedload transport will increase in MC, while it

will be lower in PC compared to the first dredging scenario. In MC, this increase will not

significantly affect the net bedload transport, which will remain less than 2 m3 per tidal

cycle (Table 12 and Tables 10-11). The net inward transport across channel transects

decreases by as much as 75% compared to the existing conditions. At the inlet however,

the flood-dominant transport for the second numerical experiment of a spatially uniform

sand bed, is predicted to double compared to the existing conditions.

Inside SBH, residual bedload transport will remain flood-dominant but

will decrease in magnitude and area (Figures 67-68, 53-54, and 31-32). However, outside

the inlet mouth in the SB channel, and especially at neap tides, the ebb-dominant residual

bedload transport patterns will intensify. The overall effect is less localized shoaling

inside SBH (a 43 – 207 m3/day decrease in accumulating bedload), and more localized

shoaling outside SBH (28 – 35 m3/day increase) compared to the existing conditions, but

also compared to the first dredging scenario. These changes after the implementation of

the second dredging scenario are markedly illustrated in the bedload divergence Figures

69-72 (and Figures 55-58, 33-36) and Figure 73 (and Figures 59, 37).

56


Floodtransport,

m3

Ebbtransport,

m3


m3

Flood to ebb ratio

First 0.0 – 0.0 0.0 – 0.0 0.0 – 0.0 N/D – N/DInlet Second 17.9 – 80.5 11.3 – 41.6 6.6 – 38.9 1.6 – 1.9 First 0.9 – 15.1 <0.0 – 1.0 0.9 – 14.1 99.5 – 15.0 PC Second 4.2 – 23.7 1.1 – 4.9 3.1 – 18.8 3.7 – 4.8 First 0.0 – 0.5 0.0 – <0.0 0.0 – 0.5 N/D – 913.7 MCSecond 0.2 – 2.9 <0.0 – 1.1 0.2 – 1.8 5.8 – 2.6


Table 12. Tidal characteristic number of bedload transport: flood to ebb ratio.Second dredging scenario. For comparison to Tables 10-11.

In the discussion that follows, comparisons are made among the three

different harbor configurations and the two numerical experiments, in regard to shoaling

of areas primarily in the interior of SBH. The bedload transport investigation presented in

this study reveals a considerable reduction of sediment volume deposited in areas

experiencing shoaling rates greater than 0.1 mm/day under neap or spring tide forcing.

Shoaling areas, associated accretion rates, and mean daily sediment volumes deposited

due to the investigated tidal processes are shown in Table 13 for each bathymetric

configuration considered here (first or second dredging scenario and existing conditions),

for each numerical experiment (varying grain size vs. sand), and for each tidal forcing

(neap – spring). These shoaling areas can be divided into two regions: the first being

inside SBH, and the second being outside the inlet in SB. Sedimentation inside from the

inlet mouth is primarily controlled by tidal processes, while outside, longshore wave

57

transport can be dominant (Hayes, 1975), but was not included in the tidal model. Thus,

Table 13 includes measurements for the same properties if only the area inside SBH is

considered.

The mean daily volume deposited on significantly shoaling areas (Table

13) was calculated by spatially integrating accretion rates over these areas. Over the

whole domain, the second dredging scenario will be associated with a 19-77 m3/day

increase in sediment fluxes to accreting areas compared to the first scenario. This is due

to a 0.22-0.28 mm/day increase in accretion rates outside the harbor’s inlet. If only the

interior of SBH is considered, bedload accretion rates for the second dredging scenario

are half of their value for the existing conditions (Table 13).

Significant shoaling areas in the entire modeling domain (include SB)Harborconfiguration

NumericalExperiment

Significantshoaling area, m2

Mean accretion rate, mm/day

Mean daily volume deposited, m3/day

Varying 93,200 – 422,600 0.98 – 2.49 91 – 1,054Existingconditions Sand 261,800 – 545,100 1.42 – 3.29 372 – 1,795

Varying 72,900 – 352,600 0.78 – 2.09 57 – 7351st dredging scenario Sand 228,900 – 469,900 1.28 – 2.77 293 – 1,299

Varying 79,000 – 361,300 0.96 – 2.25 76 – 8122nd dredging scenario Sand 213,400 – 458,900 1.54 – 3.14 329 – 1,441

Significant shoaling areas inside from the inlet mouth (only SBH)Harborconfiguration

NumericalExperiment

Significantshoaling area, m2

Mean accretion rate, mm/day

Mean daily volume deposited, m3/day

Varying 46,700 – 170,900 1.08 – 1.80 51 – 308Existingconditions Sand 102,800 – 231,800 1.82 – 2.71 188 – 627

Varying 23,000 – 110,100 0.59 – 1.28 13 – 1411st dredging scenario Sand 52,700 – 205,500 1.71 – 1.99 90 – 409

Varying 17,000 – 101,100 0.47 – 1.00 8 – 1012nd dredging scenario Sand 43,400 – 175,800 1.74 – 2.12 75 – 373

First numerical experiment: based on varying sediment types according to sediment map.Second numerical experiment: based on spatially uniform sandy bottom.Ranges shown are from neaps to spring tides (neaps – springs).Note: Volume fluxes were corrected for porosity.

Table 13. Significant (>0.1 mm/day) shoaling areas, shoaling rates, and volume fluxes.

58

An attempt to quantify these sediment fluxes for the varying sediment

(first) numerical experiment on an annual basis is presented in Table 14 and Figure 74.

The methodology used to create Table 14 and Figure 74 is presented in Appendix A-3.

Based on Table 14, at the end of a five-year period, the channels may have shoaled to an

average depth of 0.74 m (2.42 ft) below MLW from a newly dredged depth of 1.83 m (6

ft) below MLW at the beginning of that period.

Harborconfiguration

Mean annual accreting

volume, m3

Significantshoaling area,

m2

Mean annual accretion rate,

m/yearExisting

conditions 179,300 422,600 0.42

1st dredging scenario 123,000 352,600 0.35

Entiremodelingdomain(with SB) 2nd dredging

scenario 140,300 361,300 0.39

Existingconditions 60,100 170,900 0.35

1st dredging scenario 24,600 110,100 0.22

Inside from the inlet mouth(only SBH) 2nd dredging

scenario 17,300 101,100 0.17

Table 14. Comparison of mean annual accretion rates for significant shoaling areas between the existing conditions and the two dredging scenarios.

3.7.3. Inundation changes in intertidal areas.

The same methodology applied to the first dredging scenario for the

evaluation of changes in the duration of drying of intertidal shoals and marshes, was

applied to the second scenario. Figure 75, shows that low waters will again be lower (by

59

2.0-4.3 cm) inside the harbor after the removal of the shallows in south MC, as in the first

dredging scenario, and some hotspot areas will be exposed (dried) more than an

additional 4 hrs/day compared to the existing harbor configuration. On the average, the

period that intertidal areas within SBH will remain dry will increase by 0.78-1.68 hrs.

Under both scenarios there will be an approximately equal increase in the

acreage of the intertidal zone (equivalent to a decrease in the acreage of the subtidal

zone) of 10.5%; as low water elevations will drop but the high water levels will not

change among scenarios. Inside the harbor (and excluding WMC), 105,000 m2 of

previously subtidal area are predicted to start wetting and drying. The gain in intertidal

areas will be accompanied with an equal loss of subtidal areas.

60

4. Summary and recommendations for future research.

4.1. Summary and conclusions.

4.1.1. Observations.

At SB, the tide is semidiurnal: The calculated tidal form number, R, is

0.098. Between neaps and springs, M2 grew in amplitude by 65% in SB, from 0.79 m to

1.30 m: high waters became higher, while low waters became lower approximately by the

same amount (about 25 cm). Inside the harbor however, at the HoH station, the low water

level remained within ±4 cm throughout the neap to spring cycle. The high water levels at

HoH had a standard deviation of ±10 cm.

High water elevations between SB and HoH were approximately at the

same level for the period of observations, consistent with prior research. However, the

low water level rose inside the embayment. The rise of the low water level inside the

harbor is linked to attenuation of the equilibrium semidiurnal constituents M2, S2, and N2

from SB to HoH; this attenuation is even more pronounced in WMC.

4.1.2. Objective 1: Development of a numerical model to describe the

tidal hydrodynamics and explain the flood-dominant behavior of the harbor.

Since high water levels reach the same elevation in SB and HoH, the rise

in low water from SB to HoH produces a set-up in MSL inside the embayment. This set-

up ranges from 6 to 22 cm between neap and spring tides and is associated with flood-

dominant tidal asymmetry inside SBH. A zero-inertia model by Friedrichs and Madsen

(1992) explains that this behavior is primarily associated with asymmetric flood-to-ebb

61

friction due to the shallow depth of the channels. However, the use of the fully nonlinear

model ADCIRC in this study showed that advective accelerations, in addition to friction,

are important in the creation of asymmetric currents in SBH. Under the existing

conditions, these advective accelerations are most dominant in the inlet and channel

entrances, due to increased velocities there.

Under neap tides symmetric tidal dominance can occur locally. Under

spring tides however, the interior harbor retains its flood-dominant character throughout.

Similar behavior has also been reported for the Fleet, a partially vegetated tidal lagoon in

England (Robinson et al., 1983). As the tidal prism rushes through the inlet in less than 5

hrs, higher flood than ebb current speeds occur inside the embayment (flood-dominance).

Maximum, modeled depth-averaged velocities in the inlet were 1.49 m/s under neap and

2.03 m/s under spring forcing and were flood-directed.

Eulerian residual currents are directed out of the harbor, however, almost

everywhere because of the long ebb duration. Eulerian residual velocity patterns revealed

the existence of residual gyres at HoH. By residual vorticity analysis it was found that

these gyres are primarily created by vortex stretching and squeezing of the asymmetric

currents.

4.1.3. Objective 2: Description of spatial patterns of instantaneous and

residual bedload transport within the basin (existing conditions).

In SBH, residual (tidally-averaged) bedload transport patterns follow the

direction of maximum rather than residual currents because of the cubic dependency of

bedload transport on velocity. Flood dominance (net import of bedload) inside from the

62

inlet mouth of SBH is created by tidal asymmetry primarily due to friction. Ebb-

dominance (net export of bedload) outside the inlet mouth of SBH is created by the

presence of a strong ebb-jet. The interior of SBH acts as a sediment sink.

Calculating bedload transport using actual, varying sediment types, no

bedload motion is achieved inside the inlet because of the very high threshold shear stress

required for initiation of motion of the gravelly inlet bed. In the event of a storm, the sand

bluffs in SB are known to erode, leading to an increased sand load. As predicted by the

model, the locally diverging sand bedload patterns and the presence of the strong ebb jet,

prevent shoaling of the SB channel outside the harbor’s mouth and keep it self-

maintained.

Under both numerical experiments, shoaling occurs primarily in the

channels inside the embayment, on a bar attached to West Meadow Beach and on the ebb

shoal in SB. Patterns in the latter region however, may be different if longshore transport

is accounted for (e.g., Hayes, 1975).

Scouring and shoaling patterns inside SBH are similar for neap and spring

tides. Under spring tides however, the patterns spread, and bed changes become more

rapid due to faster currents and increased asymmetry. Residual bedload divergence

(scouring) and convergence (shoaling) areas are mostly confined in the channels; the

intertidal shoals and especially vegetated regions appear to be low energy environments,

largely unable to facilitate bedload motion. Northern PC and the region north of Young’s

Island are predicted to shoal most rapidly. The area south of the Stony Brook Boat Works

appears to be shoaling as well, especially during spring tides.

63

Extrapolation of the modeled shoaling rates shows that the channels could

reach their natural depth of about 61 cm (2 ft) below MLW (Cademartori, 2001) in

perhaps as soon as five years. Such long-term extrapolations are hindered however by

ADCIRC’s assumption that the bed elevation does not change significantly with time. It

is conceivable that infilling of the channel to its natural depth could lead to a state of

dynamic equilibrium due to a progressive increase in the rise of the low water level and

the creation of a positive symmetric tide through higher friction and spread of intertidal

vegetation (as may be the case for WMC).

4.1.4. Objective 3: Inundation maps of tidal flats and marshes.

Facilitated by the wetting and drying capabilities of ADCIRC, inundation

maps of tidal flats and marshes in SBH were created. Due to the constancy of low water

elevations in the interior of SBH, differences in the exposure duration (drying) of

intertidal areas between neap and spring tide forcing inside the harbor are small. A new

aerial survey may be needed to update the tidal wetlands inventory of SBH. Horse Shoe

Island for example may have shifted to the southwest since 1974, perhaps due to the

flood-dominance of the embayment.

4.1.5. Objective 4: Evaluation of proposed dredging scenarios in terms

of their impact on the existing water circulation, asymmetry, water quality, and bed

material transport.

Two proposed dredging scenarios were evaluated by altering the existing

bathymetry of the harbor and running the model on the altered domains. Both scenarios

64

included over-dredging to 3.7 m (12 ft) below MLW. In the first scenario, this dredging

was concentrated in the existing channels (MC and PC). The second scenario expanded

the first to include an extension of MC south of Young’s Island to remove the shallows

there and unite MC with PC.

Comparisons of sea level curves and least squares harmonic analysis

results from the model runs, revealed considerable changes after hypothetical dredging.

There would be a dredging-induced reduction in the magnitude of the tidal asymmetry in

SBH. The harbor would remain flood-dominant, but the relative overtide growth ratio,

M4/M2, (and thus the potential for tidal asymmetry) would reduce to about 75%-80% (for

the representative first scenario) of its existing value at HoH.

This reduction in tidal asymmetry would also be manifested in a decrease

of the duration asymmetry between the rise and fall of waters at HoH. At present, ebb

duration in the harbor is approximately 2.3 hrs (4.3 hrs) greater than flood duration under

neap (spring) tides. For the first dredging scenario, as an example, this duration

asymmetry was predicted to decrease to about 1.2 hrs under both neap and spring tides.

Limited information from WMC indicates that the bathymetric changes

that would have taken place outside this waterway would not induce considerable

changes in sea level inside the creek compared to the rest of the harbor.

For the dredged channels, the dredging-induced increase in cross-section

would tend to slow the tidal currents and decrease their ability to move sediments. At the

same time, deeper channels would decrease bottom friction, lowering the intensity of the

flood-dominant asymmetry, although increasing currents in non-dredged regions. Inside

the embayment, the overall effect would be less tidally induced shoaling.

65

The extension of the MC waterway by removing the shallows and

connecting it with PC (second scenario) would increase by approximately 17% the tidal

volume exchanged through MC. Thus velocities in MC would increase, compared to the

first dredging scenario where dredging would stop at the Stony Brook Yacht Club.

The elevation of MLW was predicted to fall some centimeters at HoH due

to less frictional dissipation of the tidal signal. As a result, average daily exposure of

intertidal flats and marshes would increase after dredging by more than one hour. That

increase would locally be more than 4 hrs/day. At the same time, the drop of low water

levels inside the harbor would cause an increase in the harbor’s intertidal area on the

order of 10% (approximately 105 m2, excluding SB and WMC).

A greater tidal prism and faster inlet velocities after dredging may increase

the sediment-sink in SBH, especially after a storm, and the increase in sand load due to

the erosion of the bluffs in SB. Assuming that sand would be available (second numerical

experiment), the net sand influx from the inlet under spring tides would double after

dredging (from 18 m3 per tidal cycle to approximately 40 m3 per tidal cycle). That

increase in sand influx might be one of the reasons for the alleged increase in shoaling of

the harbor after maintenance dredging. Other possible reasons are destabilization of

sediment during dredging, and increased undercutting and collapse of eroding, non-

dredged, intertidal regions due to faster currents. These mechanisms may be triggered

every time the harbor’s channels are subjected to manmade bathymetric alterations.

Construction of a sediment retention (“catch”) basin outside the harbor could perhaps be

one way of avoiding higher rates of import of sediment from SB, especially if deep

dredging is desired for the harbor’s interior.

66

Summarizing, Table 15 (next page) shows a comprehensive quantification

of the dredging-induced alterations predicted by the model.

67

Harbor configuration Existing conditions First dredging scenario

Second dredging scenario

Approximate Volume of sediment removed by dredging

0 585,000 m3 940,000 m3

Relative overtide growth (M4/M2) at the head of the harbor (station HoH3)Neap – spring tides

0.163 – 0.271 0.119 – 0.221 0.125 – 0.222

Relative phase difference (2Mº2 - Mº4) at the head of the harbor (station HoH3)Neap – spring tides

53.9º - 47.8º 53.1º - 40.7º 48.1º - 37.6º

Low water drop at the head of the harborNeap – spring tides

0 2.5 cm – 8.5 cm 2.0 cm – 4.3 cm

Increase in intertidal area (loss in subtidal area; excludes SB and WMC)

0 10.5% 10.5%

Mean spatially-averagedexposure change (increase in drying) of intertidal shoals and marshesNeap – spring tides

0 1.07 hrs – 1.77 hrs 0.78 hrs – 1.68 hrs

Significant (>0.1mm/day) shoaling areas under spring tides (total domain) †

423,000 m2 353,000 m2 361,000 m2

Significant shoaling areas under spring tides (inside from the inlet mouth) †

171,000 m2 110,000 m2 101,000 m2

Mean annual accreting volume on significantly shoaling areas (total) †

179,000 m3 123,000 m3 140,000 m3

Mean annual accreting volume on significantlyshoaling areas (inside) † 60,000 m3 25,000 m3 17,000 m3

Net sand influx from the inlet at spring tides ‡ 18 m3/cycle 40 m3/cycle 39 m3/cycle

† Calculation based on first numerical experiment (varying sediment types according to regional maps).‡ Calculation based on second numer. experiment (spatially uniform sandy bottom for the entire domain).

Table 15. Comprehensive quantification of dredging-induced alterations.

68

4.2. Recommendations for future research.

The model poorly simulated the tidal hydrodynamics of WMC under spring tides.

The relatively small creek is a region of large bathymetric gradients and its area is mostly

intertidal requiring very high resolution in time and space. Thus, the region can be a

difficult testing ground for shallow water hydrodynamic models with wetting and drying

capabilities.

A very important question that arises from the investigation of the dredging

scenarios is how would the predicted changes in exposure duration and associated

inundation frequencies affect the marshes in SBH. The wetlands of SBH are federally and

locally protected, and negative anthropogenic impacts on intertidal vegetation due to

dredging should be avoided.

Neither direct wind forcing, nor radiation stress was included in the model runs.

ADCIRC has the capability of including such effects. It would be interesting to

superimpose the investigated tidal processes, to those of a storm surge, or longshore

transport.

The two-fold approach used in this thesis for the estimation of bedload transport

and the divergence of its residual is built upon firm scientific background and, indeed, is

nothing else but a straightforward application of the most common research technique

used in the field. This technique however has its limitations since it is inherently

Eulerian, while sediment transport is inherently Lagrangian. Lagrangian particle-tracking

techniques have been recently developed, and although suffering from different kind of

approximations and assumptions, may be used based on the hydrodynamic output of the

SBH model (see for example, Savvidis, 2000, for a particle-tracking technique based on

69

the random walk, Lagrange-Monte Carlo, computational algorithm). These techniques

not only could provide further insight on bedload sediment transport, but also on

suspended sediment transport (which was not addressed here), as well as on contaminant

dispersion and residence times. The importance of suspended sediment transport for

sedimentation patterns in particular may increase after the over-dredging of the channels

and the predicted decrease in channel velocities (Kelley, 1980). Today, cohesive

sediment is mostly found at the head of the basin.

Figure 3. Transects for the Stony Brook Harbor Hydrographic Survey (after Cademartori, 2001). The original transects shown in this figure were expanded to include major intertidal regions (Young’s Island, Horse Shoe Island etc.), and the two creeks (West Meadow Creek and Stony Brook Creek).

72

0

1

2

3

4

5

6

7

8

9

Depth

(m be

low MS

L)

0

1

2

3

4

5

6

7

8

9

Depth

(m be

low MS

L)

Figure 6. Major Stony Brook Harbor Waterways.6a (top left): Stony Brook Harbor bathymetry (m below MSL).6b (top right): Porpoise Channel (PC) line and bathymetry of its deepest gorge.6c (bottom left): West Meadow Creek (WMC) line and bathymetry of its thalweg.6d (bottom right): Main Channel (MC) line and bathymetry of its deepest gorge.Note: All inserted bathymetric lines start from A (SB station, Figure 5).

A

A A

0

1

2

3

4

5

6

7

8

9De

pth (m

below

MSL)

A

A

B

B

C

D

D

PC Line

MC Line

AC

WMC Line

1000m

N

75

CHANNEL BASELINE LOCATIONS

Figure 8. First dredging scenario: Reconfiguration of PC and MC channels after dredging them to 3.7 m (12 ft) below MLW and after expanding PC. The figure shows locations of the two channels based on the existing channel baselines.

N500 m

77

Existingconditions

1st dredging scenario

2nd dredging scenario

Figure 9. Illustration of the second dredging scenario: The existing channels (top figure) are dredged to 3.7 m (12 ft) below MLW as in the first scenario (middle figure), but include a same depth extension of MC to meet PC (bottom figure). The grid is in meters (UTM Coordinates).

78

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80

Neap-Spring variation at Smithtown Bay (SB)

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Time (GMT)

Sea

leve

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Spring Tides Neap Tides

Figure 12. Neap to spring tide variation at SB and HoH.The spring tide shown occurred between 08/30/00 and 08/31/00.The neap tide shown occurred between 09/07/00 and 09/08/00.Note the asymmetric distortion of the tidal curve at HoH, seen in the different duration of the rise and fall of the tide there.

Neap-Spring variation at the head of the harbor (HoH)

-1.5

-1.0

-0.5

0.0

0.5

1.0

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0:00 4:00 8:00 12:00 16:00 20:00 0:00 4:00 8:00 12:00 16:00 20:00

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81

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82

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14a.

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83

Figure 15. Existing conditions: M2 amplitude (m) along the three major waterways.

M2 amplitude (m) in Porpoise Channel

0

0.2

0.4

0.6

0.8

1

1.2

1.4

0 1000 2000 3000 4000 5000 6000 7000Distance from SB, m

M 2 am

plitud

e, m

Springs Neaps

M2 amplitude (m) in WMC

0

0.2

0.4

0.6

0.8

1

1.2

1.4

0 1000 2000 3000 4000 5000Distance from SB, m

M 2 am

plitud

e, m

Neaps

M2 amplitude (m) in Main Channel

0

0.2

0.4

0.6

0.8

1

1.2

1.4

0 1000 2000 3000 4000 5000 6000 7000 8000Distance from SB, m

M 2 am

plitud

e, m

Springs Neaps

SB I1 I2 PC1 PC2 PC3 PC4 PC5 HoH1 HoH2 HoH3

SB I1 I2 MC1 MC2 MC3 MC4 MC5 PC4 PC5 HoH1 HoH2 HoH3

SB I1 I2 MC1 WMC1 WMC2-3 WMC4-5 AAC WMC6 WMC7 WMC8

84

Figure 16. Existing conditions: M2 phase (degrees) along the three major waterways.

M2 phase (degrees) in PC

0

50

100

150

200

250


M 2 ph

ase,

degre

es

Springs Neaps

M2 phase (degrees) in WMC

0

50

100

150

200

250


M 2 ph

ase,

degre

es

Neaps

M2 phase (degrees) in Main Channel

0

50

100

150

200

250


M 2 ph

ase,

degre

es

Springs Neaps




85

Figure 17. Existing conditions: M4 amplitude (m) along the three major waterways.


0

0.05

0.1

0.15

0.2

0.25

0.3


M 4 am

plitud

e, m

Springs Neaps


0

0.05

0.1

0.15

0.2

0.25

0.3


M 4 am

plitud

e, m

Neaps


0

0.05

0.1

0.15

0.2

0.25

0.3


M 4 am

plitud

e, m

Springs Neaps




86

Figure 18. Existing conditions: Z0 amplitude (m) along the three major waterways.

Zo (average sea level, m) in Porpoise Channel

0

0.05

0.1

0.15

0.2

0.25


Zero

frequ

ency

cons

tituen

t, m

Springs Neaps

Zo (average sea level, m) in West Meadow Creek

0

0.05

0.1

0.15

0.2

0.25


Zero

frequ

ency

cons

tituen

t, m

Neaps

Zo (average sea level, m) in Main Channel

0

0.05

0.1

0.15

0.2

0.25


Zero

frequ

ency

cons

tituen

t, m

Springs Neaps




87

Figure 19. Existing conditions: Relative overtide growth ratio, M4 / M2, along the three major waterways.

Relative overtide growth in Porpoise Channel

0

0.05

0.1

0.15

0.2

0.25

0.3


M 4 / M

2 amp

litude

ratio

Springs Neaps

Relative overtide growth in WMC

0

0.05

0.1

0.15

0.2

0.25

0.3


M 4 / M

2 amp

litude

ratio

Neaps

Relative overtide growth in the Main Channel

0

0.05

0.1

0.15

0.2

0.25

0.3


M 4 / M

2 amp

litude

ratio

Springs Neaps




88

Figure 20. Existing conditions: Relative phase, 2M°2 - M°4 (degrees), along the three major waterways.

2Mo2-M

o4 relative phase (degrees) in Porpoise Channel

0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Springs Neaps

2Mo2-M

o4 relative phase (degrees) in WMC

0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Neaps

2Mo2-M

o4 relative phase (degrees) in Main Channel

0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Springs Neaps




89

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 2

1. E

xist

ing

cond

ition

s: R

epre

sent

atio

n of

vel

ocity

tim

e se

ries

at S

mith

tow

n B

ay a

nd a

t the

inle

t sta

tion

I2 th

roug

h po

lar p

lots

of

dept

h-av

erag

ed v

eloc

ity m

agni

tude

. 0 d

egre

es is

UTM

Eas

t.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

90

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 2

2. E

xist

ing

cond

ition

s: R

epre

sent

atio

n of

vel

ocity

tim

e se

ries

at M

ain

Cha

nnel

sta

tions

MC

1 an

d M

C3

thro

ugh

pola

r plo

ts o

f de

pth-

aver

aged

vel

ocity

mag

nitu

de. 0

deg

rees

is U

TM E

ast.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

91

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 2

3. E

xist

ing

cond

ition

s: R

epre

sent

atio

n of

vel

ocity

tim

e se

ries

at P

orpo

ise

Cha

nnel

sta

tions

PC

2 an

d P

C4

thro

ugh

pola

r plo

ts o

f de

pth-

aver

aged

vel

ocity

mag

nitu

de. 0

deg

rees

is U

TM E

ast.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

92

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 2

4. E

xist

ing

cond

ition

s: R

epre

sent

atio

n of

vel

ocity

tim

e se

ries

at h

ead

of th

e ha

rbor

sta

tions

HoH

1 an

d H

oH3

thro

ugh

pola

r plo

ts

of d

epth

-ave

rage

d ve

loci

ty m

agni

tude

. 0 d

egre

es is

UTM

Eas

t.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

93

Figure 25. The ebb jet in the outer inlet channel is created by the pressure head between the harbor’s interior and SB. This model snapshot shows the maximum predicted pressure head during spring tides.

INLET

SB

N

300 m

94

u(M ) amplitude (m/sec) in Porpoise Channel2

0

0.2

0.4

0.6

0.8

1

1.2


u(M2)a

mplitu

de, m

/sec

Springs Neaps

u(M ) amplitude (m/sec) in Porpoise Channel4

0

0.1

0.2

0.3

0.4

0.5

0 1000 2000 3000 4000 5000 6000 7000 8000Distance from SB

u(M4) a

mplitu

de, m

/sec

Springs Neaps

Relative overtide velocity growth in Porpoise Channel

0

0.1

0.2

0.3

0.4

0.5

0.6


u(M4)/u

(M2) a

mplitu

de ra

tio

Springs Neaps

Figure 26. u(M2), u(M4) velocity amplitudes, and u(M4) / u(M2) velocity overtide growth ratio for stations along the Porpoise Channel line.Note: Amplitudes are magnitudes of the major axis of the tidal elipse for each station.

SB I1 I2 PC1 PC2 PC4 PC5 HoH1 HoH2 HoH3



95

u(M2) amplitude (m/sec) in Main Channel

0

0.2

0.4

0.6

0.8

1

1.2

0 1000 2000 3000 4000 5000 6000 7000 8000Distance from SB

u(M2) a

mplitu

de, m

/sec

Springs Neaps

u(M4) amplitude (m/sec) in Main Channel

0

0.1

0.2

0.3

0.4

0.5


u(M4) a

mplitu

de, m

/sec

Springs Neaps

Relative overtide velocity growth in the Main Channel

0

0.1

0.2

0.3

0.4

0.5

0.6

0 1000 2000 3000 4000 5000 6000 7000 8000Distance from SB

u(M4)/u

(M2) r

elativ

e ove

rtide g

rowth

Springs Neaps

Figure 27. u(M2), u(M4) velocity amplitudes, and u(M4) / u(M2) velocity overtide growth ratio for stations along the Main Channel line.Note: Amplitudes are magnitudes of the major axis of the tidal elipse for each station.

SB I1 I2 MC1 MC2 MC3 MC4 PC4 PC5 HoH1 HoH2 HoH3



96

Volume of water inside the Stony Brook Harbor Inlet.Neap Tide Simulation.

0.00E+00

2.00E+06

4.00E+06

6.00E+06

8.00E+06

1.00E+07

1.20E+07

48.1

7

50.2

0

52.2

4

54.2

7

56.3

1

58.3

4

60.3

7

62.4

1

64.4

4

66.4

8

68.5

1

70.5

4

72.5

8

74.6

1

76.6

5

78.6

8

80.7

1

82.7

5

84.7

8

86.8

2

88.8

5

90.8

8

92.9

2

94.9

5

Time in hours

Wat

er V

olum

e in

cub

ic m

eter

s

7.88E+06

2.55E+06

7.15E+06

2.62E+06

Volume of water inside the Stony Brook Harbor Inlet.Spring Tide Simulation.

0.00E+00

2.00E+06

4.00E+06

6.00E+06

8.00E+06

1.00E+07

1.20E+07

48.1

7

50.2

0

52.2

4

54.2

7

56.3

1

58.3

4

60.3

7

62.4

1

64.4

4

66.4

8

68.5

1

70.5

4

72.5

8

74.6

1

76.6

5

78.6

8

80.7

1

82.7

5

84.7

8

86.8

2

88.8

5

90.8

8

92.9

2

94.9

5

Time in hours

Wat

er V

olum

e in

cub

ic m

eter

s

10.76E+06

2.68E+06

11.15E+06

2.67E+06

Figure 29. Time series of water volume inside SBH.29a (top): Neap tides.29b (bottom): Spring tides.

98

Figu

re 3

0. S

tatio

ns s

elec

ted

for v

ortic

ity a

naly

sis

at th

e he

ad o

f the

har

bor (

V1-

V4)

.C

onto

urs

show

bat

hym

etry

(m b

elow

MS

L) a

nd v

ecto

rs in

dica

te re

sidu

al c

urre

nts

for r

efer

ence

and

com

paris

on w

ith p

revi

ous

figur

es.

99

Nea

p t

ides

Spri

ng t

ides

Figu

re 3

1. E

xist

ing

cond

ition

s: R

esid

ual B

edlo

ad T

rans

port

(m2 /d

ay) i

n S

BH

.31

a (le

ft): F

irst n

umer

ical

exp

erim

ent (

vary

ing

sedi

men

t). N

eap

tides

.31

b (r

ight

): Fi

rst n

umer

ical

exp

erim

ent (

vary

ing

sedi

men

t). S

prin

g tid

es.

1000 m

N

1000 m

N

100

Nea

p t

ides

Spri

ng t

ides

Figu

re 3

2. E

xist

ing

cond

ition

s: R

esid

ual B

edlo

ad T

rans

port

(m2 /d

ay) i

n S

BH

.32

a (le

ft): S

econ

d nu

mer

ical

exp

erim

ent (

sand

onl

y). N

eap

tides

.32

b (r

ight

): S

econ

d nu

mer

ical

exp

erim

ent (

sand

onl

y). S

prin

g tid

es.

1000 m

N

1000 m

N

101

-20

-18

-16

-14

-12

-10 -8 -6 -4 -2 0

S BI 1

I 2M C 1

M C 2

P C 3

M C 3

M C 4

M C 5

P C 4

P C 5

H o H 1

Bedload divergence(Shoaling in mm/day)

Firs

t exp

erim

ent;n

eaps

Sec

ond

expe

rimen

t;nea

psFi

rst e

xper

imen

t;spr

ings

Sec

ond

expe

rimen

ts;s

prin

gs

Figu

re 3

7. E

xist

ing

cond

ition

s: R

esid

ual b

edlo

ad tr

ansp

ort d

iver

genc

e at

sel

ecte

d m

odel

sta

tions

.Fi

rst n

umer

ical

exp

erim

ent (

vary

ing

sedi

men

t typ

es) a

nd s

econ

d nu

mer

ical

exp

erim

ent (

only

san

d).

107

Figu

re 3

9. F

irst d

redg

ing

scen

ario

: Sea

leve

l tim

e se

ries

for s

elec

ted

mod

el s

tatio

ns o

n th

e PC

line

.39

a (le

ft): N

eap

tides

.39

b (ri

ght):

Spr

ing

tides

.

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

SB I2 PC1

PC2

PC4

HoH3

39a.

39b.

Sea level (m)

109

Figu

re 4

0. F

irst d

redg

ing

scen

ario

: Sea

leve

l tim

e se

ries

for s

elec

ted

mod

el s

tatio

ns o

n th

e M

C li

ne.

40a

(left)

: Nea

p tid

es.

40b

(righ

t): S

prin

g tid

es.

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

SB I2 MC1

MC3

MC5

HoH3

40a.

40b.

Sea level (m)

110

Figu

re 4

1. C

ompa

rison

of s

ea le

vel t

ime

serie

s fo

r sel

ecte

d m

odel

sta

tions

alo

ng th

e M

WC

line

bet

wee

n ex

istin

g co

nditi

ons

and

the

first

dre

dgin

g sc

enar

io. N

eap

tides

onl

y.41

a (le

ft): E

xist

ing

cond

ition

s.41

b (ri

ght):

Firs

t dre

dgin

g sc

enar

io.

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

SB I2 WMC1

WMC2

WMC3

AAC

WMC8

41a.

41b.

Sea level (m)

111

Figure 42. First dredging scenario: M2 amplitude (m) along the three major waterways.


0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4


M 2 am

plitud

e, m

Springs Neaps


0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4


M 2 am

plitud

e, m

Neaps


0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4


M 2 am

plitud

e, m

Springs Neaps




112

Figure 43. First dredging scenario: M2 phase (degrees) along the three major waterways.

M Phase (degrees) in Porpoise Channel2

0

50

100

150

200

250


M 2 ph

ase,

degre

es

Springs Neaps

M2 phase (degrees) in WMC

0

50

100

150

200

250


M 2 ph

ase,

degre

es

Neaps

M2 phase (degrees) in Main Channel

0

50

100

150

200

250


M 2 ph

ase,

degre

es

Springs Neaps




113

Figure 44. First dredging scenario: M4 amplitude (m) along the three major waterways.


0.0

0.1

0.1

0.2

0.2

0.3

0.3


M 4 am

plitud

e, m

Springs Neaps


0.00

0.05

0.10

0.15

0.20

0.25

0.30


M 4 am

plitud

e, m

Neaps


0.00

0.05

0.10

0.15

0.20

0.25

0.30


M 4 am

plitud

e, m

Springs Neaps




114

Figure 45. First dredging scenario: Z0 amplitude (m) along the three major waterways.

Zo (average sea level, m) in Porpoise Channel

0.00

0.05

0.10

0.15

0.20

0.25


Zero

frequ

ency

cons

tituen

t, m

Springs Neaps

Zo (average sea level, m) in West Meadow Creek

0.00

0.05

0.10

0.15

0.20

0.25


Zero

frequ

ency

cons

tituen

t, m

Neaps

Zo (average sea level, m) in Main Channel

0.00

0.05

0.10

0.15

0.20

0.25


Zero

frequ

ency

cons

tituen

t, m

Springs Neaps




115

Figure 46. First dredging scenario: Relative overtide growth ratio, M4 / M2, along the three major waterways.


0.00

0.05

0.10

0.15

0.20

0.25

0.30


M 4 / M

2 amp

litude

ratio

Springs Neaps


0.00

0.05

0.10

0.15

0.20

0.25

0.30


M 4 / M

2 amp

litude

ratio

Neaps


0.00

0.05

0.10

0.15

0.20

0.25

0.30


M 4 / M

2 amp

litude

ratio

Springs Neaps




116

Figure 47. First dredging scenario: Relative phase, 2M°2 - M°4 (degrees), along the three major waterways.

2Mo2-M


0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Springs Neaps

2Mo2-M


0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Neaps

2Mo2-M


0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Springs Neaps




117

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 4

8. F

irst d

redg

ing

scen

ario

: Rep

rese

ntat

ion

of v

eloc

ity ti

me

serie

s at

Mai

n C

hann

el s

tatio

ns M

C1

and

MC

3 th

roug

h po

lar p

lots

of

dept

h-av

erag

ed v

eloc

ity m

agni

tude

. 0 d

egre

es is

UTM

Eas

t.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

118

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 4

9. F

irst d

redg

ing

scen

ario

: Rep

rese

ntat

ion

of v

eloc

ity ti

me

serie

s at

Por

pois

e C

hann

el s

tatio

ns P

C2

and

PC

4 th

roug

h po

lar p

lots

of

dep

th-a

vera

ged

velo

city

mag

nitu

de. 0

deg

rees

is U

TM E

ast.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

119

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 5

0. F

irst d

redg

ing

scen

ario

: Rep

rese

ntat

ion

of v

eloc

ity ti

me

serie

s at

Sm

ithto

wn

Bay

and

at t

he in

let s

tatio

n I2

thro

ugh

pola

r plo

ts

of d

epth

-ave

rage

d ve

loci

ty m

agni

tude

. 0 d

egre

es is

UTM

Eas

t.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

120

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 5

1. F

irst d

redg

ing

scen

ario

: Rep

rese

ntat

ion

of v

eloc

ity ti

me

serie

s at

hea

d of

the

harb

or s

tatio

ns H

oH1

and

HoH

3 th

roug

h po

lar

plot

s of

dep

th-a

vera

ged

velo

city

mag

nitu

de. 0

deg

rees

is U

TM E

ast.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

121

N

1000 m

Figure 52. Differences in tidal residual currents after the implementation of the first dredging scenario (“after dredging” - “before dredging”). Neap tides.

122

Nea

p t

ides

Spri

ng t

ides

Figu

re 5

3. F

irst d

redg

ing

scen

ario

: Res

idua

l Bed

load

Tra

nspo

rt (m

2 /day

) in

SB

H.

53a

(left)

: Firs

t num

eric

al e

xper

imen

t (va

ryin

g se

dim

ent).

Nea

p tid

es.

53b

(rig

ht):

Firs

t num

eric

al e

xper

imen

t (va

ryin

g se

dim

ent).

Spr

ing

tides

.

1000 m

N

1000 m

N

123

Nea

p t

ides

Spri

ng t

ides

Figu

re 5

4. F

irst d

redg

ing

scen

ario

: Res

idua

l Bed

load

Tra

nspo

rt (m

2 /day

) in

SB

H.

54a

(left)

: Sec

ond

num

eric

al e

xper

imen

t (sa

nd o

nly)

. Nea

p tid

es.

54b

(rig

ht):

Sec

ond

num

eric

al e

xper

imen

t (sa

nd o

nly)

. Spr

ing

tides

.

1000 m

N

1000 m

N

124

-20

-18

-16

-14

-12

-10 -8 -6 -4 -2 0

S BI 1

I 2M C 1

M C 2

P C 3

M C 3

M C 4

M C 5

P C 4

P C 5

H o H 1


Firs

t exp

erim

ent;n

eaps

Sec

ond

expe

rimen

t;nea

psFi

rst e

xper

imen

t;spr

ings

Sec

ond

expe

rimen

ts;s

prin

gs

Figu

re 5

9. F

irst d

redg

ing

scen

ario

: Res

idua

l bed

load

tran

spor

t div

erge

nce

at s

elec

ted

mod

el s

tatio

ns.

Firs

t num

eric

al e

xper

imen

t (va

ryin

g se

dim

ent t

ypes

) and

sec

ond

num

eric

al e

xper

imen

t (on

ly s

and)

.

130

Figu

re 6

1. S

econ

d dr

edgi

ng s

cena

rio: S

ea le

vel t

ime

serie

s fo

r sel

ecte

d m

odel

sta

tions

on

the

PC li

ne.

61a

(left)

: Nea

p tid

es.

61b

(righ

t): S

prin

g tid

es.

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

SB I2 PC1

PC2

PC4

HoH3

61a.

61b.

Sea level (m)

132

Figu

re 6

2. S

econ

d dr

edgi

ng s

cena

rio: S

ea le

vel t

ime

serie

s fo

r sel

ecte

d m

odel

sta

tions

on

the

MC

line

.62

a (le

ft): N

eap

tides

.62

b (ri

ght):

Spr

ing

tides

.

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

-1.5

-1.0

-0.50.00.51.01.5

4850

5254

5658

6062

6466

6870

72

Time (

hours

)

SB I2 MC1

MC3

MC5

HoH3

62a.

62b.

Sea level (m)

133

Figure 63. Second dredging scenario: Relative overtide growth ratio, M4 / M2, along the three major waterways.


0.00

0.05

0.10

0.15

0.20

0.25

0.30


M 4 / M

2 amp

litude

ratio

Springs Neaps


0.00

0.05

0.10

0.15

0.20

0.25

0.30


M 4 / M

2 amp

litude

ratio

Neaps


0.00

0.05

0.10

0.15

0.20

0.25

0.30


M 4 / M

2 amp

litude

ratio

Springs Neaps




134

Figure 64. Second dredging scenario: Relative phase, 2M°2 - M°4 (degrees), along the three major waterways.

2Mo2-M


0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Springs Neaps

2Mo2-M


0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Neaps

2Mo2-M


0

20

40

60

80

100

120


2Mo 2-M

o 4 relat

ive ph

ase,

degre

es

Springs Neaps




135

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 6

5. S

econ

d dr

edgi

ng s

cena

rio: R

epre

sent

atio

n of

vel

ocity

tim

e se

ries

at M

ain

Cha

nnel

sta

tions

MC

1 an

d M

C3

thro

ugh

pola

r plo

ts

of d

epth

-ave

rage

d ve

loci

ty m

agni

tude

. 0 d

egre

es is

UTM

Eas

t.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

136

NE

AP

TID

ES

SP

RIN

G T

IDE

S

Figu

re 6

6. S

econ

d dr

edgi

ng s

cena

rio: R

epre

sent

atio

n of

vel

ocity

tim

e se

ries

at P

orpo

ise

Cha

nnel

sta

tions

PC

2 an

d P

C4

thro

ugh

pola

r pl

ots

of d

epth

-ave

rage

d ve

loci

ty m

agni

tude

. 0 d

egre

es is

UTM

Eas

t.

N

W E

S

N

W E

S

N

W E

S

N

W E

S

137

Nea

p t

ides

Spri

ng t

ides

Figu

re 6

7. S

econ

d dr

edgi

ng s

cena

rio: R

esid

ual B

edlo

ad T

rans

port

(m2 /d

ay) i

n S

BH

.67

a (le

ft): F

irst n

umer

ical

exp

erim

ent (

vary

ing

sedi

men

t). N

eap

tides

.67

b (r

ight

): Fi

rst n

umer

ical

exp

erim

ent (

vary

ing

sedi

men

t). S

prin

g tid

es.

1000 m

N

1000 m

N

138

Nea

p t

ides

Spri

ng t

ides

Figu

re 6

8. S

econ

d dr

edgi

ng s

cena

rio: R

esid

ual B

edlo

ad T

rans

port

(m2 /d

ay) i

n S

BH

.68

a (le

ft): S

econ

d nu

mer

ical

exp

erim

ent (

sand

onl

y). N

eap

tides

.68

b (r

ight

): S

econ

d nu

mer

ical

exp

erim

ent (

sand

onl

y). S

prin

g tid

es.

1000 m

N

1000 m

N

139

-20

-18

-16

-14

-12

-10 -8 -6 -4 -2 0

S BI 1

I 2M C 1

M C 2

P C 3

M C 3

M C 4

M C 5

P C 4

P C 5

H o H 1


Firs

t exp

erim

ent;n

eaps

Sec

ond

expe

rimen

t;nea

psFi

rst e

xper

imen

t;spr

ings

Sec

ond

expe

rimen

ts;s

prin

gs

Figu

re 7

3. S

econ

d dr

edgi

ng s

cena

rio: R

esid

ual b

edlo

ad tr

ansp

ort d

iver

genc

e at

sel

ecte

d m

odel

sta

tions

.Fi

rst n

umer

ical

exp

erim

ent (

vary

ing

sedi

men

t typ

es) a

nd s

econ

d nu

mer

ical

exp

erim

ent (

only

san

d).

145

0

0.1

0.2

0.3

0.4

0.5

Existing conditions 1st dredging scenario 2nd dredging scenario

Accr

etio

n ra

te (m

/yea

r)

Inside SBH Total Domain

Existing conditions1st dredging scenario

2nd dredgingscenario

0

50,000

100,000

150,000

200,000

Accr

etin

g vo

lum

e (m

3 )

Inside SBH Total Domain

Figure 74. Comparison of mean annual accreting volumes and accretion rates between the existing conditions and the two dredging scenarios.Figure 74a (top): Mean annual accretion rate in significant shoaling areas.Figure 74b (bottom): Mean annual accreting volume in significant shoaling areas.

74a.

74b.

146

148

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154

Table of Acronyms

AAC Aunt Amy’s Creek (and respective model station).

EDT Eastern Daylight Time.

EST Eastern Standard Time.

GMT Greenwich Mean Time.

HoH Head of the harbor.

HoH1-3 Head of the harbor model stations.

I1 Inlet Station #1 (Outer inlet station).

I2 Inlet Station #2 (Inner inlet station).

KD Koppelman’s Dock (West Meadow Creek).

MC Main Channel.

MC1-5 Main Channel model stations.

MHHW Mean Higher High Water.

MHLW Mean Higher Low Water.

MHW Mean High Water.

MLHW Mean Lower High Water.

MLLW Mean Lower Low Water.

MLW Mean Low Water.

MN Mean Range.

MSL Mean Sea Level.

MSRC Marine Sciences Research Center (State University of New York at Stony Brook).

MTL Mean Tide Level.

155

NOAA National Oceanic and Atmospheric Administration.

OFC Oldfield Club (West Meadow Creek).

PC Porpoise Channel.

PC1-5 Porpoise Channel model stations.

RMS Root Mean Square.

RMSe Root Mean Square Error.

SB Smithtown Bay (and respective model station).

SBC Stony Brook Creek.

SBH Stony Brook Harbor.

SBYC Stony Brook Yacht Club.

UTC Coordinated Universal Time.

UTM Universal Transverse Mercator.

V1-4 Vorticity analysis stations for Head of the Harbor.

WMC West Meadow Creek.

WMC1-8 West Meadow Creek model stations.

WP Windell’s Pier (Head of the Harbor).

156

APPENDIX A-1

The gauges used for the collection of sea level observations in this thesis were

equipped with 100PSIA sensors. Utilization of this type of sensors in a shallow water

environment like SBH has been troublesome in the past, largely due to their design for

deep-water accuracy. A recent deployment (02/01/00-04/14/00) of such a device mounted

on a dock pile in the waters of SBYC (Figure 2), showed production of inaccurate records

of sea level when compared to ground truth measurements collected at the dock of the

Yacht Club. The deviation was found correlated to the recorded (boxcar) temperature.

For that deployment, this temperature-induced variance was removed by a correction

included in the calibration post-process, resulting in a computed standard error of 5.2 cm

(0.17 ft) (Table A-1-1, and Figure A-1-1). However, the record is still considered

unreliable. On the other hand, ground truth sea level measurements taken from Windell’s

pier and sea level calculated from the HoH gauge are well-correlated (R2=0.9998, Figure

A-1-2). Thus, the HoH data are trustworthy.

Date Time (EST) T P Baro Elev1 Observed Corr2 Corr3 Residual Remarks03/17/00 11:40:53 3.38 18.38 1034 7.65 9.75 2.10 0.00 2.1003/17/00 12:10:54 3.43 18.08 1034 6.97 9.07 2.10 0.00 2.1003/21/00 14:01:40 3.97 18.50 1028 8.12 10.24 2.12 0.00 2.1203/02/00 15:54:49 4.35 16.26 1003 3.87 3.88 0.01 0.00 0.01 omitted03/14/00 13:20:54 5.33 15.60 1024 1.69 3.75 2.06 0.00 2.0603/09/00 13:17:30 6.48 17.70 1012 6.84 8.40 1.56 0.00 1.5603/29/00 19:37:15 7.73 18.08 1010 7.76 9.14 1.38 0.00 1.3803/28/00 18:48:33 7.83 17.80 1000 7.46 7.72 0.26 0.00 0.26 omitted04/06/00 14:00:32 8.02 18.53 1015 8.62 10.16 1.54 0.00 1.5404/06/00 13:00:30 8.05 18.34 1014 8.22 9.69 1.47 0.00 1.4704/06/00 14:30:33 8.06 18.32 1015 8.14 9.68 1.54 0.00 1.5404/06/00 12:30:29 8.07 18.06 1014 7.59 9.03 1.44 0.00 1.4404/06/00 14:54:33 8.07 18.08 1015 7.60 9.09 1.49 0.00 1.4904/06/00 13:30:31 8.09 18.55 1015 8.66 10.21 1.55 0.00 1.5504/06/00 12:00:29 8.17 17.75 1014 6.88 8.37 1.49 0.00 1.4904/13/00 14:41:18 8.50 14.22 1030 -1.626 0.00 1.63 0.00 1.6304/13/00 14:47:18 8.50 14.23 1030 -1.604 0.00 1.60 0.00 1.6004/13/00 14:53:19 8.50 14.24 1030 -1.581 0.00 1.58 0.00 1.5804/13/00 14:29:18 8.54 15.74 1030 1.81 3.44 1.63 0.00 1.6304/03/00 7:40:19 9.33 16.40 1001 4.26 5.75 1.49 0.00 1.4903/02/00 15:12:48 19.35 14.73 1004 0.3805 0.00 -0.38 0.00 -0.3803/02/00 15:06:48 20.74 14.65 1004 0.1996 0.00 -0.20 0.00 -0.2003/02/00 14:36:47 20.92 14.66 1003 0.255 0.00 -0.26 0.00 -0.2603/02/00 14:42:47 21.46 14.66 1004 0.2222 0.00 -0.22 0.00 -0.2203/02/00 14:48:47 21.67 14.65 1004 0.1996 0.00 -0.20 0.00 -0.2003/02/00 14:54:47 21.78 14.65 1004 0.1996 0.00 -0.20 0.00 -0.2003/02/00 15:00:48 21.97 14.63 1004 0.1543 0.00 -0.15 0.00 -0.1503/02/00 14:18:46 23.46 14.64 1004 0.1769 0.00 -0.18 0.00 -0.1803/02/00 14:12:46 23.61 14.64 1004 0.1769 0.00 -0.18 0.00 -0.1803/02/00 14:06:46 24.03 14.63 1004 0.1543 0.00 -0.15 0.00 -0.1503/02/00 14:30:47 24.12 14.72 1003 0.3907 0.00 -0.39 0.00 -0.3901/04/00 14:24:47 24.65 14.65 1004 0.1996 0.00 -0.20 0.00 -0.20

Standard Error = 0.17 feet

Residual: Residual after tertiary correction, feet.Tertiary elevation correction coefficients calculated from graph:A0 = 2.52A1 = -0.1221

Table A-1-1. Post-calibration of Stony Brook Yacht Club Gauge.

Units and RemarksT: Temperature, degrees CP: Pressure, psiaBaro: Barometric pressure, mbarAll depths reported in feet as initially measured for precision.Elev1: Elevation, feet (first order calculated)Observed: Elevation, feet (observed)Corr2: Secondary elevation correction, feet (removal of mean difference)Corr3: Tertiary elevation correction, feet (taking temperature into account)

Tertiary calibration regressionafter exclusion of the outliers

y = -0.1221x + 2.52

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

0 5 10 15 20 25 30

Boxcar Temperature, oC

Seco

ndar

y co

rrec

tion,

ft

Outliers excludedfrom the temperature correction

This part of the recordwas taken with the gaugeout of the water

Figure A-1-1. Temperature correction of the SBYC tide gauge pressure sensor.

158

y =

0.99

9xR

2 = 0

.999

8

3.0

3.5

4.0

4.5

5.0

5.5

6.0 3.

03.

54.

04.

55.

05.

56.

0

Gau

ge-c

alcu

late

d se

a le

vel (

m)

Observed sea level (m) from Windell's Pier

Figu

re A

-1-2

. Gro

und-

truth

ing

the

HoH

tide

gau

ge.

Reg

ress

ion

betw

een

gaug

e-ca

lcul

ated

and

gro

und-

obse

rved

sea

leve

l at H

oH. T

he in

terc

ept i

n th

e re

gres

sion

was

forc

ed th

roug

h ze

ro.

159

160

APPENDIX A-2

Table A-2-1, shows the marshes of SBH in terms of approximate acreage and

mean depth below MSL. This table, in conjunction to Figure A-2-1 can provide a base for

calculation of future anthropogenic (e.g. due to dredging) or natural changes in particular

areas of interest.

Table A-2-1 was created using the GIS program Arcview (ESRI, 1999) to get the

most accurate estimate for the acreage of the individual areas shown in Figure A-2-1. The

associated ADCIRC elements created with SMS (Boss Intl., and Bringham Young

University, 2000) were brought into ArcView, selected, and their area was calculated.

Differences between the ArcView-based (ArcView Area, Table A-2-1) and SMS-based

(SMS Area, Table A-2-1) acreage are due to summation of coarse elements in the mesh.

The ArcView-based areas are the closest approximation to the true marsh acreage. Use of

SMS however, allowed for spatial integration with depth in the way of automatically

calculating volume below (Volume+, Table A-2-1) and above (Volume-, Table A-2-1)

MSL for individual areas and taking the sum of the two volumes (Volume, Table A-2-1).

Then, by dividing the resulting volume by the SMS Area, a fair approximation of the

mean depth of each individual marsh was obtained (Mean Depth, Table A-2-1).

In general, WMC marshes (Table A-2-1 and Figure A-2-1) have a higher

elevation (0.9 m above MSL) than other marshes in the harbor. WMC supports the

highest acreage of high marsh (Spartina patens) in the region of interest, which in

principle depends on very infrequent (twice a month) saltwater inundation. On the other

hand, island marshes [e.g., Young’s Island (YI) and Horse Shoe Island (HSI1-4; Table A-

161

2-1 and Figure A-2-1) are the most inundated marshes, with a mean depth of 0.6 m below

MSL. These island marshes support mostly intertidal marsh (Spartina alterniflora) which

can tolerate much more frequent (twice daily) saltwater input. Fringing marshes and the

marsh of Stony Brook Creek lie somewhere in the middle, having an average elevation of

0.3 m above MSL. Then, the island marshes will experience the predicted dredging-

induced increase in exposure duration (drying) the most when the low water in the harbor

drop. Island marshes comprised approximately one third of the total marshes in SBH in

1974 (550,000 m2, Table A-2-1).

Type

IDA

rcvi

ew A

rea

SMS

Are

aVo

lum

e+Vo

lum

e-Vo

lum

eM

ean

Dep

thD

escr

iptio

n

Mar

shSB

C38

,600

41,2

003,

800

-14,

100

-10,

300

-0.3

Ston

y B

rook

Cre

ek M

arsh

Mar

shW

MC

117

7,20

017

7,00

04,

300

-157

,200

-152

,900

-0.9

Wes

t Mea

dow

Cre

ek 1

Mar

shW

MC

211

,100

11,1

0050

0-7

,500

-7,0

00-0

.6W

est M

eado

w C

reek

2M

arsh

WM

C3

84,0

0084

,000

700

-84,

400

-83,

700

-1.0

Wes

t Mea

dow

Cre

ek 3

Mar

shW

MC

49,

500

9,00

060

0-5

,500

-4,9

00-0

.5W

est M

eado

w C

reek

4M

arsh

AAC

47,0

0046

,600

1,20

0-3

5,40

0-3

4,20

0-0

.7Au

nt A

mm

y's

Cre

ek M

arsh

Mar

shW

MC

328,

800

327,

700

7,30

0-2

90,0

00-2

82,7

00-0

.9To

tal W

est M

eado

w C

reek

Mar

shes

Mar

shJI

8,70

011

,200

Jen'

s Is

land

(Inc

lude

s A

djac

ent F

ast L

and)

Mar

shJI

8,10

09,

300

5,60

00

5,60

00.

6Je

n's

Isla

nd (O

nly

Mar

sh)

Mar

shC

I28

,800

36,7

0021

,200

021

,200

0.6

Com

mar

ge Is

land

Mar

shM

arsh

HSI

114

7,50

014

4,80

089

,500

089

,500

0.6

Hor

she

Sho

e Is

land

Mar

sh 1

Mar

shH

SI2

35,8

0032

,500

21,7

000

21,7

000.

7H

orsh

e S

hoe

Isla

nd M

arsh

2M

arsh

HSI

37,

400

22,0

0011

,300

011

,300

0.5

Hor

she

Sho

e Is

land

Mar

sh 3

Mar

shH

SI4

8,90

022

,000

14,1

000

14,1

000.

6H

orsh

e S

hoe

Isla

nd M

arsh

4M

arsh

YI36

8,40

043

2,60

0Yo

ung'

s Is

land

Mar

shYI

270,

800

334,

900

191,

600

-17,

900

173,

700

0.5

Youn

g's

Isla

nd (O

nly

Mar

sh)

Mar

shM

I42

,600

66,4

0059

,100

059

,100

0.9

"Mar

ina

Isla

nd" M

arsh

Mar

shN

I2,

500

10,0

003,

000

03,

000

0.3

"Nep

tune

's Is

land

" Mar

shM

arsh

Isla

nds

552,

400

678,

600

417,

100

-17,

900

399,

200

0.6

Tota

l Sto

ny B

rook

Har

bor S

alt M

arsh

Isla

nds

(Mar

sh o

nly)

Mar

shEB

M19

9,10

026

8,40

027

,600

-92,

500

-64,

900

-0.2

East

Bou

ndar

y M

arsh

Mar

shSB

M72

,500

128,

700

20,6

00-4

5,50

0-2

4,90

0-0

.2So

uth

Boun

dary

Mar

shM

arsh

WB

M66

,300

69,8

00W

est B

ound

ary

Mar

sh (I

nclu

des

Inte

rnal

Fas

t Lan

d)M

arsh

WB

M65

,300

68,9

008,

500

-20,

200

-11,

700

-0.2

Wes

t Bou

ndar

y M

arsh

(Onl

y M

arsh

)M

arsh

NB

M17

2,10

017

7,40

015

,100

-122

,000

-106

,900

-0.6

Nor

th B

ound

ary

Mar

shM

arsh

LBM

M1,

000

2,30

050

0-3

0020

00.

1Lo

ng B

each

Mar

ina

Mar

shM

arsh

DSM

131,

200

160,

100

Dre

dge

Spoi

l Mar

sh (I

nclu

des

Inte

rnal

Fas

t Lan

d)M

arsh

DSM

125,

500

154,

300

27,1

00-4

7,80

0-2

0,70

0-0

.1D

redg

e Sp

oil M

arsh

(Onl

y M

arsh

)M

arsh

SBM

M38

,000

62,3

005,

100

-27,

400

-22,

300

-0.4

Smith

tow

n Ba

y M

arin

a M

arsh

Mar

shB

ound

arie

s67

3,50

086

2,30

010

4,50

0-3

55,7

00-2

51,2

00-0

.3To

tal S

tony

Bro

ok H

arbo

r Frin

ging

Mar

shes

(Onl

y M

arsh

)

Tota

l Mar

shSB

H1,

264,

500

1,58

2,10

052

5,40

0-3

87,7

0013

7,70

00.

1To

tal S

tony

Bro

ok H

arbo

r Mar

shes

Tota

l Mar

shSB

H+W

MC

1,59

3,30

01,

909,

800

532,

700

-677

,700

-145

,000

-0.1

Tota

l Mar

shes

(Gra

nd T

otal

)

Reg

ion

WM

C56

6,10

056

1,60

026

3,60

0-3

02,1

00-3

8,50

0-0

.1W

est M

eado

w C

reek

Reg

ion

SBH

4,62

2,40

04,

622,

400

Ston

y Br

ook

Har

bor (

Incl

udes

Inte

rnal

Fas

t Lan

d)R

egio

nSB

H4,

517,

600

4,50

9,80

04,

525,

300

-426

,100

4,09

9,20

00.

9St

ony

Broo

k H

arbo

r (Ex

clud

es In

tern

al F

ast L

and)

Reg

ion

SB88

,480

,100

88,5

23,6

001,

093,

160,

400

-27,

500

1,09

3,13

2,90

012

.3Sm

ithto

wn

Bay

Tota

l Reg

ion

93,6

68,6

0093

,707

,600

1,09

3,42

4,00

0-3

29,6

001,

093,

094,

400

11.7

Tota

l Dom

ain

(Incl

udes

Inte

rnal

Fas

t Lan

d &

Dre

dge

Spoi

ls)

Tota

l Reg

ion

93,5

63,8

0093

,595

,000

1,09

7,94

9,30

0-7

55,7

001,

097,

193,

600

11.7

Tota

l Com

puta

tiona

l Dom

ain

Wat

er B

ody

WM

C23

7,30

023

3,90

024

7,20

0-1

4,10

023

3,10

01.

0W

est M

eado

w C

reek

Tha

lweg

(Gor

ge)

Wat

er B

ody

SBH

3,25

3,10

02,

927,

700

3,99

9,90

0-3

8,40

03,

961,

500

1.4

Ston

y Br

ook

Har

bor (

incl

udes

inte

rtida

l sho

als

and

mud

flats

)W

ater

Bod

ySB

88,4

80,1

0088

,523

,600

1,09

3,16

0,40

0-2

7,50

01,

093,

132,

900

12.3

Smith

tow

n Ba

y (in

clud

es in

terti

dal s

hoal

s an

d m

udfla

ts)

Tabl

e A

-2-1

. Are

as a

nd m

ean

dept

hs o

f mar

shes

, geo

grap

hica

l reg

ions

and

wat

er b

odie

s re

lativ

e to

this

pro

ject

.

Not

e: A

ll un

its a

re S

I (ar

ea: m

2 , vol

ume:

m3 , d

epth

: m b

elow

mea

n se

a le

vel).

Ple

ase

refe

r to

Figu

re A

-2-1

to id

entif

y lo

catio

ns o

f int

eres

t bas

ed o

n ID

.

164

APPENDIX A-3

Model results generally showed that areas shoaling during neap tides, expand

under spring tides, but largely retain their positions on the bedload divergence maps

(Figures 33-36, 55-58, 69-72). Based on this observation, we assumed a linear relation

between time and significant shoaling areas (areas with shoaling rates greater than 0.1

mm/day), as well as a linear correlation between time and shoaling rates. As an example,

consider the second dredging scenario with varying sediment and the domain only inside

from the inlet mouth. Assume the first day of the year to be a neap day. Then, the 8th day

will be a spring day (and the 15th again a neap). For these days, the shoaling area,

accretion rate, and sediment volume flux are known from Table 13 and are:

Day Area

m2

Rate

mm/day

Sediment

Flux

m2*mm/day

1 (neap) 16,977 0.47 7,976

… … … …

8 (spring) 101,088 1.00 101,204

Through linear interpolation for areas and rates independently with time (or

number of days) the same parameters for days 2 through 7 were calculated. Next, the

expected sediment flux (equal to the product of shoaling area times shoaling rate) was

computed:

165

Day Area

m2

Rate

mm/day

Sediment

Flux

m2*mm/day

1 (neap) 16,977 0.47 7,976

2 28,993 0.55 15,822

3 41,009 0.62 25,492

4 53,025 0.70 36,986

5 65,040 0.77 50,304

6 77,056 0.85 65,447

7 89,072 0.93 82,413

8 (spring) 101,088 1.00 101,204

To close the neap-spring cycle, days 9-14 were added, which were assumed the

same as days 2-7 in reverse order:

Day Area

m2

Rate

mm/day

Sediment

Flux

m2*mm/day

1 (neap) 16,977 0.47 7,976

2 28,993 0.55 15,822

3 41,009 0.62 25,492

4 53,025 0.70 36,986

5 65,040 0.77 50,304

6 77,056 0.85 65,447

7 89,072 0.93 82,413

8 (spring) 101,088 1.00 101,204

9 89,072 0.93 82,413

10 77,056 0.85 65,447

11 65,040 0.77 50,304

12 53,025 0.70 36,986

13 41,009 0.62 25,492

14 28,993 0.55 15,822

This cycle repeats itself about 365/14 (=26.071) times. Equivalently, there will

be 26.071 number-1 days in the year, 26.071 number-2 days etc. Then, a crude estimate

of the sediment volume that would be “deposited” annually on the shoaling areas inside

166

from the inlet mouth for the second dredging scenario was gained by multiplying the

sediment fluxes above by 26.071 days, and adding the resulting volumes:

Day Area

m2

Rate

mm/day

Sediment

Flux

m2*mm/day

Sediment

Volume

m3

1 (neap) 16,977 0.47 7,976 208

2 28,993 0.55 15,822 412

3 41,009 0.62 25,492 665

4 53,025 0.70 36,986 964

5 65,040 0.77 50,304 1,312

6 77,056 0.85 65,447 1,706

7 89,072 0.93 82,413 2,149

8 (spring) 101,088 1.00 101,204 2,639

9 89,072 0.93 82,413 2,149

10 77,056 0.85 65,447 1,706

11 65,040 0.77 50,304 1,312

12 53,025 0.70 36,986 964

13 41,009 0.62 25,492 665

14 28,993 0.55 15,822 412

Mean Annual Accreting Volume (m3): 17,262

The mean annual accretion rate for significant shoaling areas was then

calculated by dividing the mean annual accreting volume calculated above (17,262 m3)

by the largest extent of the significantly shoaling areas under spring tides (in this case

equal to 101,088 m2). Results are presented in Table 14 and Figure 74.

tidal hydrodynamics and bedload transport in a shallow ......york, usa) provided a description of...

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