Lower Cherry Aqueduct Emergency Rehabilitation Project

Hydrology Technical Memo

November 6, 2014

Prepared by: Kelley Capone, Chris Graham, and Adam Mazurkiewicz Introduction The proposed action, the Lower Cherry Aqueduct Emergency Rehabilitation (LCAER) Project consists of rehabilitation of and construction of improvements to the existing nearly-100-year-old Lower Cherry Aqueduct (LCA) by the San Francisco Public Utilities Commission (SFPUC). The proposed action would restore the historic design capacity of the LCA to provide reliable delivery of water stored at Lake Eleanor and Cherry Reservoir into the Hetch Hetchy Water and Power System to supplement San Francisco Bay Region water supply during severe droughts. Under the proposed action the LCA would be operated for up to 4 months annually during severe droughts and would deliver up to 48,000 acre-feet of water to SFPUC’s customers. An acre foot of water is the volume of water that covers one acre to a depth of one foot. An acre foot of water is equivalent to 325,851 gallons. The SFPUC operates the Regional Water System under the Water First Policy which focuses operations on maximizing carryover storage such that risks to water supply are minimized. The Water First operational policy was instituted in response to extreme water shortages during water years (WY) 1987 through 1992, the most recent extended drought. This policy has been implemented in system operations since 1993. Under this policy use of the stored water for power generation may be curtailed in order to minimize risks to water supply and it is under these conditions that the use of the LCA may be needed for water conveyance. Lake Eleanor and Cherry Reservoir are connected by a pipeline and the two reservoir storage volumes are operated as one unit of storage under the Water First Policy. When stored water is in short supply or climatic conditions threaten a supply shortage, the Water First Policy may require use of Cherry and Eleanor for water supply. The project would be constructed in two phases. The majority of the rehabilitation and improvement would take place during Phase 1, in spring and summer 2015, and would include the following elements, which would ensure the reliable transport of 165 cfs—the present system capacity-- through the existing system. Phase 1 project elements would include:

• Replacement of open canal sections with large-diameter buried pipe and improved connections to tunnel segments to prevent entry of soil and debris from steep slopes above and eliminate hazards to people and animals traveling near the canal

• Restoration and replacement of deteriorated elements at Cherry Creek Diversion Dam • Restoration of the access trail to the Cherry Creek Diversion Dam • Improvements to an existing concrete forebay tank for pipeline inspection and

maintenance • Import of up to 22,000 cy of fill and soils from one or more locations, including optional

use of an existing borrow site at Granite Portal, within the Stanislaus National Forest.

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Phase 2 would be designed in 2016 and constructed in 2019. Phase 2 would consist of geotechnical assessment of the pipeline location and replacement of 300-linear feet of existing 72-inch-diameter pipeline with an 84-inch diameter pipeline or siphon in the same alignment to restore the 200-cfs historical design capacity of the aqueduct. This report focuses on identifying the environmental consequences of operating the LCA at 200 cfs. Operation of the LCA allows access to water in Cherry Reservoir and Lake Eleanor to serve as water supply in the Bay Area. When LCA operations are implemented, water would first be released from Lake Eleanor. Lake Eleanor can supply the LCA diversion for approximately two months at a rate of 200 cfs. Water would be released directly from Lake Eleanor into Eleanor Creek. If diversions through LCA were desired beyond the period Lake Eleanor could supply, water from Cherry Reservoir would be released directly to Cherry Creek for diversion to the LCA. The overall volume during a month period is approximately 12,000 acre-feet at a rate of 200 cfs. The longest period of time in which LCA is anticipated to be used is four months within the November – March timeframe, resulting in a maximum total volume of 48,000 acre-feet of water diverted through the LCA. Throughout the operation of LCA, the instream release requirements (Table 4) below Cherry Reservoir and Lake Eleanor would be maintained below the Cherry Creek Diversion Dam. Use of the LCA would occur during the late fall and winter of dry years during periods of sustained drought. The period of operation would vary depending on operational need, hydrologic conditions, system conditions, and optimization of the water supply system, but is not planned to exceed 4 months within the November – March timeframe. The purpose of this report is to provide information on hydrologic effects that could result from construction and operation of the LCAER project. Hydrologic effects resulting from construction and operation of the LCAER project on reservoir levels, streamflow, and non-point source pollution are identified by evaluating measures including but not limited to temperature, sedimentation, habitat, and ground disturbance. 1. Analysis Framework: Statute, Regulations, Forest Plan, and Other Direction

The SFPUC manages two reservoirs that feed the Lower Cherry Aqueduct (LCA) as part of the Hetch Hetchy Regional Water System (HHRWS): Cherry Reservoir on Cherry Creek (a tributary of the Tuolumne River) and Lake Eleanor on Eleanor Creek (a tributary of Cherry Creek). Lake Eleanor lies within Yosemite National Park, while Cherry Reservoir and most of the downstream drainage are within the Stanislaus National Forest. Protection of water quality is an important part of the mission of the Forest Service (USDA 2007). Management activities on National Forest lands must be planned and implemented to protect the hydrologic functions of forest watersheds, including the volume, timing, and quality of streamflow. A number of Federal and State regulations and policies guide construction projects on National Forest Service lands as well as water operations on California Rivers. The Clean Water Act (CWA) of 1948 (as amended in 1972 and 1987) establishes federal policy for the control of point and non-point pollution, and assigns the states the primary responsibility for control of water pollution. Compliance with the CWA by National Forests in California is achieved under state and federal law, as described below. The National Best Management

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Practices for Water Quality Management on National Forest System Lands (USDA 2012) identifies Best Management Practices (BMPs) for the protection of waters and water quality. Best management practices incorporated in the LCAER Project are identified in Attachment C to this memo. The US Army Corps of Engineers regulates activities in or affecting waters of the United States under Section 404 of the CWA, including fill for development, water resource projects (such as dams and levees), infrastructure development (such as highways and airports) and mining projects. Section 404 requires a permit before dredged or fill material may be discharged into waters of the United States, unless the activity is exempt from Section 404 regulation (e.g. certain farming, forestry, maintenance and emergency activities). The State/Regional Water Resources Control Board implements the State's Water Quality Certification (WQC) Program, which was formally initiated in 1990 in response to the requirements of Clean Water Act (CWA) 401, under the CWA and the Porter-Cologne Water Quality Act, as amended in 2006. Issuing WQC for discharges requiring U.S. Army Corps of Engineers' Section 404 permits for fill and dredge discharges is a core responsibility. If a Section 404 permit is not required, the Regional Water Resources Control Board may issue a Waste Discharge Requirement to permit a project to proceed. State and Regional Water Boards assess water quality monitoring data for California’s surface waters every two years to determine if they contain pollutants at levels that exceed protective water quality standards. Water body and pollutants that exceed protective water quality standards are placed on the State’s 303(d) List. This determination in California is governed by the Water Quality Control Policy for developing California’s Clean Water Act Section 303(d) List. The State/Regional Water Resources Control Board adopted ambient standard for a surface or ground water body. The standard covers the beneficial use of the water and the water quality criteria that must be met to protect the designated use or uses. The Tuolumne Wild and Scenic River Management Plan (USDA 1988) provides direction for managing the federal lands within the boundaries of the designated Tuolumne River corridor. This plan was prepared by the Forest Service, for those portions of the Tuolumne Wild and Scenic River outside of Yosemite National Park, and identifies river values to be protected. Tuolumne Wild and Scenic River Management Plan river values associated with hydrology include Free-Flowing Condition and Water Quality. The Stanislaus National Forest Plan Direction (April 2010, amended 2012) (Forest Plan) provides forestwide standards and guidelines as well as management area directives applicable to specific land classifications within the Forest. Forest Plan standards and guidelines related to water resources are provided in Attachment A. Attachment A also identifies the Land Allocation Area of Riparian Conservation Areas and associated standards and guidelines. 2. Effects Analysis Methodology

Analyses in this report are based on watersheds delineated in accordance with the national watershed classification system (Table 1) (USGS 2013), which identifies the Hydrologic Unit Code (HUC) for each watershed. The HUC classifies watershed by size. The project is located in two HUC Level 5 and two HUC Level 6 watersheds (see Table 2). Beneficial uses of water and water quality objectives in the California Water Quality Control Plan (Basin Plan) of the Central Valley Regional Water Quality Control Board (CVRWQCB 2011) were utilized as a benchmark regarding the existing condition and to access the effects of the

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proposed action on water quality. Beneficial uses for the Tuolumne River surface water listed in the Basin Plan are municipal and domestic supply; irrigation; stock watering; power; contact; canoeing and rafting; other non-contact recreation ; warm water habitat; cold water habitat ; and wildlife habitat. The water quality parameters considered in the water quality analysis were reservoir levels, water temperature, and sediment related parameters. 2.1 Assumptions Specific to Watershed and Environmental Indicators and Measures The following are assumptions specific to the watershed:

1. The project area includes existing facilities to store and deliver water for domestic and municipal use. Cherry Creek and Eleanor Creek are within the project study area and are streams with flows controlled by upstream dams.

2. The Lower Cherry Aqueduct (LCA) is an existing water transport facility, and the proposed project would rehabilitate the LCA to restore its historical design capacity.

3. Substantial portions of the project watershed were severely burned in the Rim Fire of 2013.

4. Minimum instream release requirements (Table 4) and flows to meet downstream flow obligations will continue to be met.

5. Water Quality Best Management Practices will be implemented as part of the project to protect water quality during any ground-disturbing activities. (Attachment C)

The hydrologic analysis considers the following indicators and measures:

1. Indicator: Reservoir Water Level. Measures: temperature, water elevation compared to previous elevations, habitat.

2. Indicator: Stream Flows. Measures: temperature, changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, sediment transport, degrade riparian vegetation and habitats, and groundwater and near stream water table effects.

3. Indicator: Non-Point Source Pollution. Measures: amount of ground disturbance, construction stormwater, erosion/sedimentation, and release of hazardous construction materials/fuels.

Streamflow effects will consider the magnitude (the amount of change per unit of space and time), extent (how vast is the change), direction (how dynamic is the change), duration (how lasting is the change), and speed (how rapid is the change). 3. Affected Environment 3.1 Watershed Description Watersheds in the national forest are delineated in accordance with the national watershed classification system (USGS 2013). The classification system uses the term Hydrologic Unit Code (HUC) to describe watershed size and class. Table 1 illustrates how the system applies to watersheds in the project area.

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Table 1 Hydrologic Unit Code (HUC)

HUC Level HUC Name HUC Size

(average acres) HUC Example LCA Project

areas 1 Region 100,000,000 NA 2 Sub-region 10,000,000 NA 3 Basin 7,000,000 San Joaquin River 4 Sub-basin 450,000 Tuolumne River 5 Watershed 40,000-250,000 Cherry Creek 6 Sub-watershed 10,000-40-000 Lower Cherry Creek 7 Drainage 2,000-10,000 Granite Creek 8 Sub-drainage Less than 2,000

The Stanislaus National Forest includes HUC Level 4 through 8 watersheds. HUC Level 4 watersheds on the Forest are the headwaters of major rivers that continue downstream off the forest. HUC Level 5 watersheds on the Forest are associated with the tributaries of these large rivers. While some HUC Level 5 watersheds on the forest extend somewhat downstream and upstream from the forest boundaries most are entirely within the forest. Construction of the LCAER Project would take place entirely within the Lower Cherry Creek HUC Level 6 watershed; however, operational effects are evaluated in Lower Cherry Creek and Miguel-Eleanor Creek HUC level 6 watersheds shown in Table 2. Operational effects are changes in reservoir levels and stream flows as a result of operating the LCA. The study area for project effects related to hydrology is larger than the construction area because the hydrologic effects can occur in reservoirs and streams outside of the construction area.

Table 2

Principal Watersheds in the LCAER Project Area HUC Level 5 (40,000 – 250,000 Acres) HUC Level 6 (10,000 – 40,000 Acres)

Name Acres Name Acres Cherry Creek 90,892 Lower Cherry Creek 24,383 Eleanor Creek 59,906 Miguel-Eleanor Creek 15,798 3.2 Watershed Characteristics The Tuolumne River drains a HUC Level 4 watershed on the western slope of the Sierra Nevada range and is the largest of three major tributaries to the San Joaquin River. The mainstem of the river originates in Yosemite National Park and flows southwest to its confluence with the San Joaquin River, approximately 10 miles west of Modesto. The LCA project construction is within the Lower Cherry Creek HUC Level 6 sub-watershed. LCA operational effects related to hydrology are within the Lower Cherry Creek and Miguel-Eleanor Creek HUC Level 6 sub-watershed. The watershed extends from the crest of the Sierra Nevada Mountains near 10,800 feet to the Cherry Creek Diversion Dam at 2,630 feet. 3.2.1 Climate Mean annual precipitation in the Cherry Creek and Eleanor Creek watersheds ranges from 30 inches to greater than 50 inches in the high mountains (as measured in annual snow surveys). The watershed is in a Mediterranean climate with hot, dry summers and cool, wet winter periods

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(Figure 1). The winter storm season may begin as early as October and extend into May. Typically winter snowline is near 5,500 feet but varies from year to year. The snow transition zone is between 4,000 and 5,500 feet elevation, with frequent snow events in the winter, though the snow accumulation may ablate. Snow events at elevations as low as 2,000 feet occur nearly every year. Annual variation in precipitation and hydrologic conditions results in a large disparity in annual runoff – ranging from 20% to 250% of the annual average. This variation is controlled by the snow accumulation during the winter season, as typically 75% of the annual runoff occurs during the April through July snowmelt period.

Figure 1: Climograph for the Cherry Reservoir meteorological station located near Cherry Valley Dam at an elevation of 4800 feet. 3.2.2 Geology and Geomorphology

Along with a wide range in elevation, the watersheds have a large variation in soil structure and geology. At higher elevations (6,000-10,800 feet), the watershed was scoured by glaciers during the Tioga and earlier glacial periods, and is characterized by exposed granitic bedrock, with steep mountains and deep canyons. Eleanor Creek has been frequently glaciated and has shallow soils and exposed granitic bedrock. The gradient for Eleanor Creek ranges from 2 – 6.1 percent. Cherry Creek has large boulders over granite bedrock, with cobble, gravel, and sand lee behind large boulders and bedrock outcrops. The gradient for Cherry Creek ranges from 2 – 5 percent Attachment B provides additional information on the geomorphology of Eleanor and Cherry Creeks. Soils within the project area are primarily derived from metamorphic rock and granitic rock. The dominant soils within the study area are mostly loams, sandy loams, and loamy sands with gravelly to extremely gravelly texture modifiers, indicating high natural infiltration rates, and high rock content in many areas. These soils range from shallow to deep, reflecting a wide range of soil productivity and soil hydrologic groups.

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3.2.3 The Water Landscape The water landscape in the LCA Project area includes two water supply reservoirs (described in Section 4.1) and two principal creeks. Streams in the National Forest have a Riparian Conservation Area (RCA) of 300 feet on each side of the stream measured from bankfull edge of the stream (USDA 2010). See the Wetland Delineation and Preliminary Jurisdictional Determination report for a description of wetlands in the project area. 3.2.3.1 Eleanor Creek The section of Eleanor Creek within the study area that would be used to convey water for the LCA Project begins at Lake Eleanor Dam and flows south west for approximately 3.5 miles to the confluence with Cherry Creek. Attachment B, Figure 6-1 provides a profile of this section of Eleanor Creek showing the channel gradient downstream of Eleanor Dam. Attachment B also provides a description of steam morphology and characteristics. Water temperature in the creek is controlled by water temperature at the outlet level in Lake Eleanor. 3.2.3.2 Cherry Creek Two sections of Cherry Creek within the study area would be used to convey water for the LCA Project. Cherry Creek below Cherry Valley Dam to the confluence with Eleanor Creek, which is approximately 4.4 miles, and Cherry Creek from the confluence with Eleanor Creek to the Cherry Creek Diversion Dam, which is approximately 4.1 miles. Attachment B provides a description of steam morphology and characteristics. Water temperature in the creek is controlled by water temperature at the outlet level in Cherry Lake. 3.2.4 Vegetation Communities The vegetation community affected by the LCA project operations includes riparian vegetation along the segments of creeks described above. Lower elevations (2,200-6,000 feet) are dominated by coniferous forest which begin to transition to oak dominated forests. Riparian vegetation associated with Eleanor Creek has established along and above the channel as a result of flood peaks passing over the dam and flowing down the creek. The flood peaks scour the channel and inhibit riparian woody plant encroachment. Evidence of frequent riparian woody plant scour was observed and species diversity and location is comparable to unregulated Sierra Nevada streams. Riparian vegetation associated with Cherry Creek from the dam to the confluence with Eleanor Creek has been influenced by Cherry Valley Dam’s reduction of peak flood flows. Riparian encroachment was evident at some locations. Species diversity and location is comparable to regulated Sierra Nevada streams with large storage reservoirs. Riparian vegetation associated with Cherry Creek below the confluence with Eleanor Creek is similar to riparian vegetation associated with Eleanor Creek because this section of Cherry Creek experiences the peak flood flows from Eleanor Creek. Attachment B provides additional information on the vegetation communities associated with Cherry and Eleanor creeks. 4. Existing Watershed Facilities

The SFPUC operates a series of reservoirs, tunnels, pipelines, powerhouses and other facilities in the Sierra Nevada Mountains of Tuolumne County, CA, to store and deliver water to the City and County of San Francisco and 26 wholesale customers in the San Francisco Bay area. One such facility, the LCA, is used to deliver water stored in Lake Eleanor and Cherry Reservoir to the Bay

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Area for domestic and municipal use. The water conveyed by the LCA from Cherry Reservoir and Lake Eleanor augments the water supply in the Regional Water System. This section describes the Lake Eleanor and Cherry Reservoir system and summarizes the existing facilities of this portion of the HHRWS. The hydrologic results of operation of the LCA as proposed as related to reservoir levels and flows in Cherry and Eleanor creeks are presented in Section 7. Data related to reservoir operations and releases during a period of dry hydrologic conditions is provided in Section 6 to demonstrate system operations during drought without use of LCA, as a base case condition. 4.1 Reservoirs and Facilities

The HHRWS operates three storage reservoirs within the Tuolumne River Sub-Basin: Hetch Hetchy Reservoir on the Tuolumne River, Lake Eleanor on Eleanor Creek (a tributary of Cherry Creek) and Cherry Reservoir (also known as Lake Lloyd or Cherry Lake) on Cherry Creek (a tributary of the Tuolumne River). These reservoirs are operated as a portion of the entire HHRWS which includes five storage reservoirs in the San Francisco Bay Area as well as an extensive water distribution network and two water treatment plants. The HHRWS serves water to 2.6 million people and the Tuolumne River Basin provides approximately 85% of the water supply for the service area. Lake Eleanor, Cherry Reservoir and associated facilities are relevant to the analysis of the LCAER project and are described below. 4.1.1 Lake Eleanor Lake Eleanor Dam is located in Yosemite National Park and was completed in 1918. The reservoir impounds a maximum capacity of 27,100 acre-feet at an elevation of 4661 feet with 1.49 square miles of surface area. The reservoir is located on Eleanor Creek approximately 3.5 miles upstream from the confluence with Cherry Creek. The reservoir is open to public access including non-motorized boating and swimming. Water can be transferred from Lake Eleanor in two ways: 1) released to Eleanor Creek, which flows into Cherry Creek and can be diverted at Cherry Creek Diversion Dam into the LCA, or 2) transfer to Cherry Reservoir through the one mile-long Lake Eleanor Diversion Tunnel. The tunnel is described below in Section 4.1.4. Eleanor Dam has four valves that release water to Eleanor Creek. The spillway has a capacity of 15,000 cubic feet per second (cfs) to allow excess inflow to pass during snowmelt runoff and storm events. CFS is a unit expressing the rate of flow of water. One cubic foot per second is equal to the discharge through a rectangular cross-section one foot wide and one foot high, flowing at an average velocity of one foot per second. One cubic foot per second equals 448.8 gallons per minute, and 1.98 acre-feet per day. Therefore, 15,000 cfs equates with about 29,750 acre-feet per day. 4.1.2 Cherry Reservoir Cherry Valley Dam is located in the Stanislaus National Forest and was completed in 1956. The dam impounds Cherry Reservoir with a maximum capacity of 273,400 acre-feet at an elevation of 4702.5 feet with 2.80 square miles of surface area. The reservoir is located on Cherry Creek approximately 4.4 miles upstream of the confluence with Eleanor Creek. The reservoir is open to public access, including motorized boating and swimming.

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Water is transferred from Cherry Reservoir in two ways: 1) released directly to Cherry Creek then diverted at Cherry Creek Diversion Dam into the LCA with a portion allowed to continue downstream to meet minimum instream release requirements, or 2) diversion to Holm Powerhouse (HPH) through Cherry Creek Tunnel, then released to Cherry Creek and allowed to continue downstream for storage at Don Pedro Reservoir to meet flow obligations to the districts. Cherry Valley Dam has four valves to release water to Cherry Creek. The spillway at Cherry Reservoir, which has a capacity of 52,000 cfs is only used during extreme high water events because the reservoir has sufficient capacity to contain most or all inflows during a typical year. Table 3: Reservoir descriptions

Reservoir Year

completed Watershed

Area (sq. mi.)

Watershed Elevation

Range (feet) Reservoir Capacity

(acre-feet)

Median Annual Inflow

(acre-feet) Lake Eleanor 1918 78 4,650-10,400 27,100 168,000

Cherry Reservoir 1956 117 4,700-10,800 273,400 273,000

4.1.3 Lake Eleanor Diversion Tunnel The Lake Eleanor Diversion Tunnel connects Lake Eleanor with Cherry Reservoir, and allows water to be transferred to Cherry Reservoir for power generation at HPH. The tunnel can also be used to transfer water via gravity when Cherry Reservoir is lower than Lake Eleanor. The tunnel has a regulatory daily transfer limit of 1,000 acre-feet. 4.1.4 Cherry Creek Tunnel The Cherry Creek Tunnel connects Cherry Reservoir with HPH. Water is transferred from Chery Reservoir through the Cherry Creek Tunnel to HPH for power generation. 4.1.5 Cherry Creek Diversion Dam The Cherry Creek Diversion Dam and head gate structure is located in Cherry Creek approximately 4.1 miles downstream of the Cherry Creek and Eleanor Creek confluence. The Cherry Creek Diversion Dam impounds less than 15 acre-feet and is used only for diversion, not for water storage. From the diversion dam head gates, water is conveyed via tunnels and open channels to Early Intake Reservoir on the Tuolumne River. 4.1.6 Holm Powerhouse HPH is located approximately 11 miles downstream of Cherry Reservoir on Cherry Creek, 0.75 miles upstream of Cherry Creek’s confluence with the mainstem of the Tuolumne River. The powerhouse has a maximum draft capacity of approximately 950 cfs (about 1,885 acre-feet per day), which is supplied from Cherry Reservoir via the Cherry Creek Tunnel. Water drafted from Cherry Reservoir through HPH is released to Cherry Creek at the powerhouse, eventually merging with the mainstem of the Tuolumne River and continuing downstream to Don Pedro Reservoir. 4.1.7 Lower Cherry Aqueduct The LCA allows the HHRWS to transfer water from Cherry Reservoir and Lake Eleanor to the HHA for delivery to the Bay Area. Stored water released to Cherry Creek (or Eleanor Creek to

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Cherry Creek) from either reservoir is diverted into the LCA via the Cherry Creek Diversion Dam. From the diversion dam head gates, water is conveyed via tunnels and open channels to Early Intake Reservoir on the Tuolumne River, where it can enter the Mountain Tunnel and HHA. The design capacity of the LCA is approximately 200 cfs and the current operation capacity is approximately 165 cfs.

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Figure 2: Schematic of Tuolumne River System, USGS station numbers are noted for reference.

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Figure 3. Map of Cherry and Eleanor Creeks and LCA Project area.

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5. Description of Current Operations Due to the Lake Eleanor Diversion Tunnel connecting Cherry Reservoir and Lake Eleanor, the two reservoir storage volumes are operated as one unit of storage. The HHRWS system is operated under the SFPUC’s Water First Policy. Under the Water First Policy HHRWS operations focus on maximizing carryover storage such that risks to water supply are minimized. The stored water at Cherry and Eleanor comprises a portion of the total system storage. When stored water is in short supply or climatic conditions threaten a supply shortage, the Water First Policy may require use of Cherry and Eleanor for water supply. Use of the stored water for power generation may be curtailed in order to minimize risks to water supply and it is under these conditions that the use of the LCA may be needed for water conveyance. The upstream reservoirs capture flows from the upper portion of the watershed, which reduces the overall instream flow rates in Cherry Creek even during normal and above normal water years. However, fall and winter storms have resulted in occasional releases from Cherry Reservoir and frequent spills at Lake Eleanor, especially during non-drought years. As a result flow in Cherry Creek at the Cherry Creek Diversion Dam can vary greatly from mid-October to mid-July. The minimum condition observed during the November through March period under existing operations in most years is less than 10 cfs, while maximum rates during storm events is greater than 4,000 cfs. 5.1 Lake Eleanor Given the large contributing area and small storage capacity of Lake Eleanor, annual snowmelt runoff has filled the reservoir every year in the historical record. This allows the HHRWS to transfer water to Cherry Reservoir for power generation at HPH, resulting in a seasonal cycling of Lake Eleanor. The extent of this seasonal cycling is limited by a requirement under a stipulation agreement between SFPUC and Yosemite National Park to maintain an elevation in Lake Eleanor at or above 4651 feet in elevation from the end of snowmelt runoff (approximately June) through September 30th for recreational purposes. The minimum water elevation in non-summer months is at or above 4630 feet in elevation. Most years, after September 30th, water is transferred to Cherry Reservoir via the Lake Eleanor Diversion Tunnel to become available for power generation at Holm Powerhouse. Water can continue to be pumped to Cherry Reservoir through December 31st. Pumping cannot re-commence after January 1st until Lake Eleanor has filled and spilled 50 cfs. As a result the reservoir fills through winter months, until either a large warm storm occurs or snowmelt runoff begins in earnest. Once Lake Eleanor fills and spills, pumping from Lake Eleanor to Cherry Reservoir continues until snowmelt runoff stops. After this time Lake Eleanor elevation is maintained at or above the summer elevation target of 4651 feet. 5.2 Cherry Reservoir Cherry Reservoir’s large storage capacity, small contributing area and the transfer of water from Lake Eleanor results in a somewhat steady reservoir level throughout the fall and winter months (Figure 4). During normal hydrologic conditions, snowmelt runoff would bring the reservoir to near capacity during spring runoff and reservoir elevation is managed through HPH. During a dry water year, the reservoir level may not reach capacity, but storage would be maintained at the highest elevation possible while meeting instream flow requirements and the City’s flow obligations to the districts through releases at HPH. While reservoir elevations at Cherry Reservoir are not subject to stipulations requiring minimum water elevations, the reservoir is typically drawn down 10 to 15 feet from its peak elevation at the end of snowmelt runoff over the summer period with small daily variations.

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5.3 Instream Releases Lake Eleanor and Cherry Reservoir have instream release requirements (Table 4) which maintain and protect fish, wildlife and recreation. Lake Eleanor’s stipulated agreement is with the Department of Interior as of 1982, while Cherry Reservoir instream flow agreement is with the Department of Agriculture as of 1950. Releases are monitored at United States Geologic Survey (USGS) stream gaging stations below each reservoir (Figure 2) (gaging stations 1127730 and 1127800). The required releases remain in the channel, but are subject to evaporation loss and loss to groundwater and subsurface flow. At the confluence of Cherry Creek and Eleanor Creek the flows combine and continue down Cherry Creek to the Cherry Creek Diversion Dam approximately 4.1 miles downstream. Flow below the Cherry Creek Diversion Dam is measured at a USGS gaging station approximately 1.8 miles downstream (, gaging station 1127830). Table 4: Instream release requirements in cubic feet per second Oct Nov-Feb Mar Apr May June July-Aug Sept Lake Eleanor (when pumping occurs) 10 5 10 10/20 20 20 20 20/10 Lake Eleanor (when pumping does not occur) 5 5 5 5 5 5 15.5 15.5 Cherry Reservoir 5 5 5 5 5 5 15 15 Total 15 10 20 15-25 25 25 25-35 35-25 5.4 Recreational Flows for River Boating Summertime flow patterns are controlled by releases made through HPH and are shaped to provide recreational flows for river boating downstream of HPH. These releases are made for 4-hours per day at the maximum available draft rate for approximately 29 days per month between Memorial Day weekend and Labor Day weekend. HHRWS has shaped releases to provide these non-regulatory flows in coordination with rafting groups since the early 1990’s. The timing, rate, and duration of the releases have varied based on operational restrictions, hydrologic conditions, and energy regulations and contracts. The current structure of the recreational release program (4-hours per day between 0700 hours to 1100 hours) has been in place since 2005. 5.5 Regional Hydrology and Reservoir Management In most years, water in Lake Eleanor and Cherry Reservoir is used to maintain the SFPUC’s flow obligations to the senior water right holders on the Tuolumne River – Turlock and Modesto irrigation districts (collectively referred to as the districts). Water is also released during the snowmelt runoff period (generally the spring months) to manage reservoir elevation, and is primarily routed through the Cherry Creek Tunnel to HPH to generate power, then released to Cherry Creek. Water is also released from each reservoir throughout the year to meet instream ecological release requirements described in Section 5.3. During extreme droughts, the water from Lake Eleanor and Cherry Reservoir can also be delivered to the Bay Area through the LCA. Irrespective of seasonal or drought conditions or the use of LCA, the SFPUC is required to meet its flow obligations to the districts and instream release requirements. Due to the precipitation pattern and hydrologic condition described in Section 3 above, reservoir management typically focuses on the April through July snowmelt period. Given the small

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storage capacity of Lake Eleanor in comparison to annual inflow (Table 3) the reservoir fills every year and releases of stored water in excess of capacity typically occur. In contrast, the storage capacity of Cherry Reservoir is sufficient to accommodate typical annual runoff volumes. Given the draft capacity at HPH, releases at Cherry Valley Dam in excess of the instream release requirements typically only occur during above-normal runoff conditions. 5.6 Maintenance Cherry Reservoir and Lake Eleanor have periodically been drawn down to perform maintenance work. Major maintenance at Cherry Reservoir entails drawing the level down to 4536 feet (166 feet below maximum elevation). More frequently, Cherry Reservoir is drawn down to 4611 feet to perform maintenance at the Cherry-Eleanor Pump Station. The most recent drawdown for maintenance work was the fall of 2007. Cherry Reservoir water elevation has been drawn down for maintenance three times since 1993. Water elevation has been drawn down for maintenance or has been lower due to drought conditions five times since 1983. During the 1987 – 1992 drought Cherry Reservoir was extremely low and was almost empty in 1988. Lake Eleanor is drawn down to 4622 feet approximately every 10 to 15 years for maintenance work. This may include an early season draw down to ensure work can be completed prior to fall storm events. The most recent draw down of Lake Eleanor for maintenance work was during the fall of 2011. 6. Example of Drought Operations – Water Years 2012 through 2014 The HHRWS Water First operational policy was instituted in response to extreme water shortages during water years (WY) 1987 through 1992, the most recent extended drought. This policy has been implemented in system operations since 1993. System operations during WY 2012-2014 are used to demonstrate Water First operations during extended drought conditions. WY 2012 through 2014 is the driest three-year sequence over the period of record (1919-present). While significant storm events occurred during this period, each year had below normal precipitation (55% to 75% of normal). The impacts of operations on reservoir elevations and releases during the WY 2012 through 2014 are described below. 6.1 Reservoir Levels 6.1.1 Cherry Reservoir Initial high storage levels and Water First operations at Cherry Reservoir prior to the current drought period resulted in relatively high storage levels during WY 2012, which were maintained until the cessation of snowmelt runoff (Figure 4). The reservoir was then slowly drawn down through the summer and fall months. A winter storm in December 2012 resulted in an increase in storage level, which was maintained throughout the winter. As a result, the reservoir neared capacity during the snowmelt runoff period of 2013. During the summer and fall of 2013 and winter of 2014 the reservoir was drawn down as water was released to meet instream release requirements and flow obligations to the districts, while inflows were limited. While meeting these obligations, the HHRWS was able to shape releases at HPH to provide for recreational rafting. During the snowmelt runoff period reservoir storage increased but did not reach capacity. Throughout the summer of 2014 the reservoir continued to be drawn down. As the result of limited inflows and the operations described, during the third year of the drought sequence the reservoir was approximately 25 feet lower ( approximately elevation 4700 feet to 4675 feet) than the first year of the drought.

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Figure 4: Cherry Reservoir storage and elevation. 6.1.2 Lake Eleanor Lake Eleanor operations throughout WY 2012-2014 period were similar to those during normal hydrologic conditions. Early in WY 2012 the reservoir was drawn down for maintenance work and the reservoir subsequently refilled during snowmelt runoff. Storage remained high through the summer of 2012 and into the winter of WY 2013 due to storm events. The reservoir was then maintained at or above elevation 4651 feet through the summer of WY 2013 for recreation and pumped down during the fall and winter months, refilling during runoff of WY 2014. The pattern observed during WY 2014 (pumping from October into December, refilling from January through February, and pumping during the snowmelt runoff period – March through May) is typical for average to dry conditions. In contrast, if conditions were extremely wet the fall and winter drawdown of Eleanor by transfer to Cherry Reservoir through the Lake Eleanor Diversion Tunnel may not occur due to limited available storage at Cherry Reservoir.

Figure 5: Lake Eleanor storage and elevation. Facility repairs necessitated draining of the reservoir during the fall of 2011.

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6.2 Releases 6.2.1 Eleanor Creek Releases from Lake Eleanor into Eleanor Creek are common, a result of the limited storage capacity of the reservoir in comparison to the snowmelt runoff volume and limited pumping capacity for transfer of water to Cherry Reservoir. This results in spill (water in excess of storage or diversion) during periods of high inflow and snowmelt runoff (Figure 6). Flow rates in Eleanor Creek during snowmelt runoff exceeded 1,500 cfs during WY 2012, and a peak flow greater than 3,000 cfs occurred during an early winter storm. In contrast, during the WY 2014 snowmelt period releases remained mainly below 500 cfs, with a peak near 1,000 cfs. During periods outside of snowmelt runoff and storm events, required instream releases were maintained (Table 4).

Figure 6: Eleanor Creek streamflow below Eleanor Dam (USGS Station 11278000).

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6.2.2 Cherry Creek below Cherry Reservoir to the Eleanor Creek Confluence Cherry Reservoir water level elevation is typically managed through power generation at HPH. Most years, water is released into Cherry Creek directly below Cherry Reservoir only as needed to meet the instream release requirements. However, during the late fall of WY 2013 water was released from Cherry Reservoir into Cherry Creek to manage reservoir elevation during storm events. During brief periods, releases at the dam were increased as needed to perform maintenance on release valves. (Figure 7) Release rates from Cherry Valley Dam exceeded the minimum instream release requirement during the snowmelt runoff regularly. Flows in Cherry Creek have exceeded 2000 cfs during three events in 2011 and exceeded 3000 cfs during an event in 2010. Flows in Cherry Creek regularly exceed 400 cfs.

Figure 7: Cherry Creek streamflow below Cherry Valley Dam (USGS Station 11277300).

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6.2.3 Cherry Creek below the Eleanor Creek Confluence The flow at the Cherry Creek Diversion Dam includes accretions from watershed areas below Cherry Reservoir and Lake Eleanor, but is dominated by instream releases from the reservoirs. This is generally due to the small contributing area (~20,000 acres) and low elevation range of the contributing area below the reservoirs. Accretions during the summer period can be negligible as seen during the WY 2012 through 2014 period (Figure 8). During years when there are limited releases from Cherry Reservoir, the hydrograph below the confluence is similar to the hydrograph below Eleanor Dam (compare hydrographs in Figure 6 and Figure 8). As a result, during the snowmelt the hydrograph is dominated by the pattern of release from Lake Eleanor, while the remainder of the season reflects instream release requirements. A large flow of nearly 4000 cfs did occur during the early winter of 2013 due to a large rain on snow event which resulted in releases from Lake Eleanor and Cherry Reservoir, as well as substantial accretions.

Figure 8: Cherry Creek streamflow downstream of the Cherry Creek and Eleanor Creek confluence (USGS Station 11278300).

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6.2.4 Cherry Creek below Holm Powerhouse The flow in Cherry Creek below HPH throughout most of the year is controlled by operations at HPH, although the snowmelt runoff can dominate the hydrograph shape as shown during the spring of 2012 (Figure 9). This is a result of consistent releases through HPH during the snowmelt runoff period in order to manage reservoir elevation at Cherry Reservoir. Summertime patterns are controlled by releases made through HPH and are shaped to provide recreational flows for river boating downstream of HPH as described in Section 4.3.

Figure 9: Cherry Creek streamflow below HPH (USGS Station 11278400).

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6.2.5 The Mainstem of the Tuolumne River below the Cherry Creek confluence The flow in the mainstem of the Tuolumne River at the confluence of Cherry Creek (Figure 10) reflects the releases from Hetch Hetchy Reservoir, Lake Eleanor, Cherry Reservoir, and HPH. Throughout the summer and fall months, the flow pattern strongly reflects operations at HPH and the provided recreational release pattern. Outside of this period, flows reflect reservoir and powerhouse releases except during storm events when significant accretions can occur. During the snowmelt runoff period, spill and releases from the reservoirs can dampen the signal of HPH operations, similar to the runoff season of 2012. However, during an extremely dry year (WY 2014) flow patterns are mainly driven by releases from HPH.

Figure 10: Calculated flow on the Tuolumne River below the Cherry Creek confluence (the summation of USGS Station 11278400 and USGS Station 11276900).

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7. Use of Lower Cherry Aqueduct and Environmental Consequences This section identifies the environmental consequences of the LCAER project related to the following indicators and measures:

1. Indicator: Reservoir Water Level. Measures: temperature, water elevation compared to previous elevations, habitat

2. Indicator: Stream Flows. Measures: temperature, changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, sediment transport, degrade riparian vegetation and habitats, and groundwater and near stream water table effects.

3. Indicator: Non-Point Source Pollution. Measures: amount of ground disturbance, construction stormwater, erosion/sedimentation, and release of hazardous construction materials/fuels.

Streamflow effects will consider the magnitude (the amount of change per unit of space and time), extent (how vast is the change), direction (how dynamic is the change), duration (how lasting is the change), and speed (how rapid is the change). The following analysis of hydrologic effects includes effects of project construction and operations. The LCAER Project would be implemented in two phases. The first phase focuses on replacing open culvert sections of the LCA with pipelines and other minor work to achieve approximately 165 cfs capacity of LCA. Phase 2 of the LCAER Project would restore the LCA design capacity of 200 cfs. The environmental consequences of operating the LCA at 200 cfs are presented below. Operation of the LCA allows the HHRWS to access water in Cherry Reservoir and Lake Eleanor to serve as water supply in the Bay Area for municipal and domestic use. Municipal and domestic water supply is one of the beneficial uses of water identified in the Basin Plan (CVRWQCB 2011). When LCA operations are implemented, water would first be released from Lake Eleanor. Lake Eleanor can supply the LCA diversion for approximately two months at a rate of 200 cfs. Water would be released directly from Lake Eleanor into Eleanor Creek. If diversions through LCA were desired beyond the period Lake Eleanor could supply, water from Cherry Reservoir would be released directly to Cherry Creek for diversion to the LCA. The overall volume during a month period is approximately 12,000 acre-feet at a rate of 200 cfs. The longest period of time in which LCA is anticipated to be used is four months within the November – March timeframe, resulting in a maximum total volume of 48,000 acre-feet of water diverted through the LCA. Throughout the operation of LCA, the instream release requirements (Table 4) below Cherry Reservoir and Lake Eleanor would be maintained below the Cherry Creek Diversion Dam. Use of the LCA would occur during the late fall and winter of dry years during periods of sustained drought. The period of operation would vary depending on operational need, hydrologic conditions, system conditions, and optimization of the water supply system, but is not planned to exceed 4 months within the November – March timeframe due to the limitations discussed above. The effect of the LCA on streamflow pattern under the existing conditions (streams with dams and reservoir operations) is presented below to provide a context of the net change in the flow regime in each section of stream channel. Calculated flow with no dams on the creeks (an estimate of natural flow conditions without reservoirs in the system) is also provided to compare the LCA release rate to the natural hydrology.

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7.1 Construction Effects – Construction Areas Construction effects related to hydrology could create non-point source pollution, an environmental indicator. Non-point source pollution could affect waters, water quality wetlands, and soils. Measures related to this environmental indicator include amount of ground disturbance, construction stormwater, erosion/sedimentation, and release of hazardous construction materials/fuels. A non-point source of pollution is any source of pollution including sedimentation or hazardous substances that is not originating from a point source. Construction stormwater and erosion/sedimentation measures are addressed below in Section 7.11 under sediment transport. Non-point source pollution of hazardous substances could be created by maintaining or refueling construction equipment in areas where a release of hazardous materials could enter waters adjacent to the construction area. This addresses the measures of the amount of ground disturbance and the release of hazardous construction materials/fuels. Best Management Practices (BMPs) Fac-6 and Fac-7, identified in Attachment D, would reduce the potential for non-point source pollution by requiring training, refueling and maintenance activities to take place in areas that would not result in releases of fuels or construction materials to water bodies, preparation of a spill prevention and countermeasure plan, and appropriate handling of vehicle and equipment wash water. Construction of the LCAER project would not result in an impact to non-point source pollution releases of hazardous material because the project will comply with the Forest Plan and BMPs will be implemented for the project. Construction is not proposed to take place within wetlands; therefore, the proposed action would not have a direct effect on wetlands. 7.2 Streamflow Effects The environmental indicator of stream flow includes measures that evaluate temperature, changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, sediment transport, degrade riparian vegetation and habitats, and groundwater and near stream water table effects. The following sections address streamflow effects for each segment of stream in the study area. Temperature is addressed in section 7.10 and sediment transport is addressed in section 7.11. Because Cherry and Eleanor Creeks commonly experience flows higher than 200 cfs as part of normal operations, effects related to changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, degrade riparian vegetation and habitats, and groundwater and near stream water table are not anticipated from operation of this project under the proposed action because the proposed release rate of 200 cfs is lower than higher flows that are commonly experienced. Each section of stream in the study area is discussed below. 7.3 Streamflow Effects – Eleanor Creek For the proposed action, streamflow in Eleanor Creek would increase during periods of release for LCA diversion over existing conditions. However, flow increases during these releases are typically within the lower end of range of flows experienced by the stream. In the absence of releases for the LCA, under “normal” operations, typically releases from Eleanor Dam during November through March (the period of potential LCA operations) would not exceed the minimum instream release requirements (Table 4). During periods when LCA releases would be made from Lake Eleanor, flows in Eleanor Creek would be approximately 200 cfs greater than

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when LCA is not in operation. For LCA operation, releases from Lake Eleanor would extend for no more than a two month duration due to operational restrictions and the lack of storage capacity to meet LCA diversions for a longer period of time. Although Eleanor Creek would experience increased flow during the LCA operation period, the increase would be within the range of flows experienced seasonally during drought periods (note December 2012 period in Figure 6). The 200 cfs increase in flow above the instream release requirement to provide LCA releases results in approximately a 2.3 foot increase in stage at the USGS gaging station. The increase in stage would vary throughout the stream corridor. At the USGS cross sectional measurement location for higher flows, the change in stage is estimated to be greater than at the gage station due to the channel confinement. For comparison, the increase in stage at both locations is not expected to reach bankfull. As described in Section 6.2.1, the section of Eleanor Creek below Eleanor Dam has experienced flows of approximately 500 cfs or greater during snowmelt periods within the last three years and typically surpasses 1,000 cfs during snowmelt. Construction and operation of the LCAER project would not result in impacts related to changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, degrade riparian vegetation and habitats, and groundwater and near stream water table effects because the increase flow would be within the range of flows experienced seasonally. 7.4 Streamflow Effects – Cherry Creek below Cherry Reservoir to the Eleanor Creek Confluence If water shortages in the system required LCA diversions for more than two months, releases from Cherry Reservoir would be made under LCA operations. In the absence of LCA operations, typical releases during November through March (the period of potential LCA operations) do not exceed the minimum instream release requirements (Table 4). During periods when LCA releases would be made from Cherry Reservoir, flows in Cherry Creek would be approximately 200 cfs greater than would typically occur. Although Cherry Creek would experience increased flow during the period of LCA operations, flows up to 200 cfs are not uncommon during this time of year during “normal” (i.e. non-drought) periods. Infrequently during times of drought the creek can experience flows in excess of 150 cfs and up to greater than 500 cfs during storm events (Figure 7). The 200 cfs increase in flow to provide LCA releases results in a 1.47 ft. increase in stage at the USGS gaging station. The change in stage would be different in different sections of the creek depending on channel conditions; however, estimates of increased stage are not expected to reach bankfull. Construction and operation of the LCAER project would not result in impacts related to changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, degrade riparian vegetation and habitats, and groundwater and near stream water table effects because the increase flow would be within the range of flows experienced seasonally. 7.5 Streamflow Effects – Cherry Creek below the Eleanor Creek Confluence Regardless of which reservoir water is released from, flows in Cherry Creek below the Cherry and Eleanor creek confluence above the Cherry Creek Diversion Dam would increase over existing conditions during operation of the LCA. Flow in this section of creek typically remain slightly above instream release requirements during the fall and winter months in Cherry Creek due to flow accretions (Figure 8). Flow in Cherry Creek at the Cherry Creek Diversion Dam can vary greatly from mid-October to mid-July. The minimum condition observed during the November through March period under existing operations in most years is less than 10 cfs, while maximum rates during storm events is greater than 4,000 cfs (Figure 11). The estimated release

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rate of 200 cfs for LCA plus instream release requirements (Table 4) would result in an increase over the normal seasonal flow during operation of LCA, but falls within the bounds of flows during snow melt under the current operational conditions (reservoirs in operation) . The increase in flow from operation of LCA in the November through March timeframe is within the existing range of flows experienced under current conditions with the dam in place. An estimate of what natural flow conditions would be without the presence of HHRWS facilities were calculated to provide a comparison of the LCA operations under existing conditions to what the condition would be if dams and reservoirs were not existing conditions (Figure 12). Streamflow with the assumption that dams and reservoirs are not existing is calculated by adding the change in storage to releases then adding an estimate of evaporation. While the release rate for LCA falls within the range of existing conditions (Figure 11) during the November – March time period, the release rate is in the lower range of calculated flow assuming no dams and reservoirs on the creeks (Figure 12). Calculated streamflow assuming no dam and reservoir on the creek within this section of Cherry Creek during the fall and winter months are consistently higher than existing flow rates (Figure 12). In a normal year, median daily flow increases from approximately 75 cfs in November to approximately 750 cfs in March as snowmelt runoff begins. Throughout the fall and winter season flows can vary greatly depending on storm events. The estimated release rate for LCA operations falls within the calculated bounds of the minimum and median conditions assuming no dams and reservoirs on the creeks, trending near the lower limit of flow conditions assuming no dams and reservoirs on the creeks.

Figure 11: Historical streamflow in Cherry Creek below the Cherry Creek and Eleanor Creek confluence. Dashed line indicates LCA diversion rate (200 cfs) plus instream release requirements.

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Figure 12: Calculated streamflow in Cherry Creek below the Cherry Creek and Eleanor Creek confluence assuming no dams and reservoirs on the creeks. Dashed line indicates LCA diversion rate (200 cfs) plus instream release requirements. Construction and operation of the LCAER project would not result in impacts related to changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, degrade riparian vegetation and habitats, and groundwater and near stream water table effects because the increase flow would be within the range of flows experienced seasonally. 7.6 Streamflow Effects – Cherry Creek below Cherry Creek Diversion Dam LCA operation on streamflow below Cherry Creek Diversion Dam would have no impact. Releases below the Cherry Creek Diversion Dam would be maintained to equal the combined required releases from each reservoir (Table 4) and the estimated accretions. Any additional water released to Cherry and Eleanor creeks for the LCA would be diverted to the LCA upstream of this reach. Flow would be monitored at the USGS gage approximately 1.8 miles downstream of the diversion dam (USGS Station 11278300). Construction and operation of the LCAER project would not result in impacts related to changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, degrade riparian vegetation and habitats, and groundwater and near stream water table effects because no change in flow below Cherry Creek Diversion Dam is anticipated from LCA operations. 7.7 Streamflow Effects – Cherry Creek below HPH Releases to Cherry Creek below HPH would continue to contribute to meet the SFPUC flow obligation to the districts. The water release though HPH would continue to be shaped to maximize efficiency for power operations and recreational flows as possible. As a result there is no anticipated change to streamflow in Cherry Creek below HPH during the operation of the LCA project. Construction and operation of the LCAER project would not result in impacts related to changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, degrade riparian vegetation and habitats, and groundwater and near stream water table effects because no change in flow below HPH is anticipated during LCA operations.

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7.8 Streamflow Effects – The Mainstem of the Tuolumne River below the Cherry Creek

confluence This section of the river is controlled by flows from upstream on the Tuolumne River and facility releases from the reservoirs and HPH. Instream release requirements (Table 4) would be maintained as well as releases from HPH to meet the SFPUC’s flow obligations to the districts. As a result there is no anticipated change in streamflow on the mainstem of the Tuolumne River below the Cherry Creek confluence due to operation of the LCA project. Construction and operation of the LCAER project would not result in impacts related to changes to stream channel (geomorphic changes, channel incision, scouring, and erosion), flooding, degrade riparian vegetation and habitats, and groundwater and near stream water table effects because no change in flow in the Tuolumne River is anticipated during LCA operations. 7.9 Reservoir Elevation Effects The environmental indicator of reservoir water level includes measures of temperature, water elevation compared to previous elevations, and habitat. Temperature is addressed in section 7.10. The overall impact of LCA operations on reservoir elevations would be dependent on reservoir management and hydrologic conditions leading up to the operation of the LCA. With or without implementation of the LCAER Project, the reservoir elevation at Cherry Reservoir would fall throughout drought periods (Figure 4), while Lake Eleanor would maintain the typical seasonal pattern as a result of meeting summer elevation targets (Figure 5). As the overall system storage becomes stressed from drought conditions, reservoir storage levels would be maximized (maintained at the highest elevation possible) to maintain system storage levels and to provide water for diversion to the LCA to the extent possible. Operation of the LCA would use water within Lake Eleanor as the first volume to be diverted in the fall or early winter. This operation is similar to historical seasonal operations of lowering the reservoir during the late fall and winter (Figure 5) through pumping water to Cherry Reservoir. However, when LCA is in operation, pumping from Lake Eleanor to Cherry Reservoir would be reduced commensurately with total anticipated LCA releases at Lake Eleanor. Reduction in the amount of water transferred from Lake Eleanor would result in lower Cherry Reservoir levels. If additional water was needed, releases would be made from Cherry Reservoir. As a result LCA deliveries could cause a partial drawdown of Cherry Reservoir (Figure 13). Potential reservoir level outcome scenarios from the operation of LCA for various periods of time are discussed below and illustrated in Figure 13 and Figure 14. An example of anticipated drought conditions under critically dry conditions (99% exceedance level) is used to present potential reservoir level outcomes under five different LCA use scenarios (“No LCA” use and 1 through 4 months of use). The prospective drought scenario uses the August 1, 2014 reservoir levels and appends the lowest inflows on record. Under the assumed dry conditions, operation of LCA at 165 cfs may be necessary in fall and winter 2014 due to limited inflow. Under the base case of “No LCA Use”, Lake Eleanor is drawn down (Figure 14) as water is transferred to Cherry Reservoir. This water transfer allows for Cherry Reservoir elevation to be maintained (Figure 13). If operation of the LCA requires one month of operation, Lake Eleanor

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would initially be held high during the fall and water then released to the LCA when it is needed. The remainder of available storage would be transferred to Cherry Reservoir following the conclusion of LCA operations. If water supply required two months of LCA diversions, Lake Eleanor would be held high during the fall and released for diversion by LCA, resulting in a lower water level at Cherry Reservoir due to the reduced volume of water transfer. If operations required three or four months of LCA diversions, the water would be taken first from Lake Eleanor for two months then from Cherry Reservoir for the remainder of the period. Due to the seasonal transfer of water from Lake Eleanor to Cherry Reservoir under existing conditions and the filling of Lake Eleanor during snowmelt runoff, the seasonal water level in Lake Eleanor would be almost the same with implementation of LCA operations as it would be if LCA operations were not implemented. Effects of reservoir elevations in Lake Eleanor related to the measures of water elevation compared to previous elevations and changes to habitat are not anticipated from operation of this project. Cherry Reservoir elevation would be lowered 6 to 30 feet by LCA operation, depending on the duration of use of the LCA (Figure 13). This example illustrates a difference from the “base case” and does not necessarily reflect absolute resultant elevations. The true outcome would be dependent on antecedent conditions and operations required over the previous years to meet the SFPUC’s flow obligations to the districts. While Cherry Reservoir elevation would be affected by the LCA operations, the decrease in water elevation is within the range of elevations experienced during normal operations including maintenance. Effects of reservoir elevations in Cherry Reservoir related to the measures of water elevation compared to previous elevations and changes to habitat are not anticipated from operation of this project. Construction and operation of the LCAER project would not result in impacts related to changes in water elevation compared to previous elevations and shoreline habitat because reservoir levels would be within historic operations elevation ranges.

Figure 13: Cherry Reservoir elevation conditions under the potential LCA use scenarios. The bars represent the month of modeled LCA use.

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Figure 14: Lake Eleanor elevation conditions under the potential LCA use scenarios. The bars represent the month of modeled LCA use.

7.10 Water Temperature Effects Water temperature in Cherry and Eleanor creeks are controlled by the water temperature at the outlet level in Cherry Reservoir and Lake Eleanor. Cherry Reservoir is a relatively large lake and the supply for the release valves is low in the reservoir (272 feet below the maximum water surface elevation). The high thermal capacity of the large lake, combined with the low outlet, results in relatively consistent low seasonal water temperatures (Figure 15). Lake Eleanor is much smaller than Cherry Reservoir and the release valves are closer to the surface (approximately 42 and 56 feet below water surface at full pool depending on valve position). The reduced thermal capacity leads to greater temperature variation within the lake, resulting in higher temperature variation in released water (Figure 15). Temperature conditions within Lake Eleanor under LCA operations are not expected to vary from historical conditions. This is due to the similar pattern of reservoir elevation under operations of the LCA as compared to “normal” operations. Lake Eleanor would seasonally refill and the elevation would be maintained through the summer months. Some slight variation in temperature pattern could occur due to the timing of drawdown; however, because maintaining the reservoir elevation would not change there is no anticipated change in the temperature pattern. Under LCA operations water temperature conditions in Cherry Reservoir would also remain relatively unchanged. This is due mainly to the large volume of water (thermal mass), which would buffer any effects. The potential deceased water level due to LCA operations is within the range of water levels experienced during normal operations and maintenance As described in Section 5.3 Cherry Reservoir is drawn down to elevation 4611 feet to perform maintenance on the

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Cherry-Eleanor Pump Station. The extended drought period with warm, dry days would have a more significant impact on lake water temperature than any change in lake volume. However, these effects would also be anticipated to be slight given the overall storage volume within Cherry Reservoir and the relative constant temperature of snowmelt runoff. Once released, water temperature is controlled by ambient air temperatures and the relative mixing volumes from Cherry and Eleanor creeks. Stream temperature measured below the Cherry Creek and Eleanor Creek confluence are usually bounded by the temperatures of the two upstream tributaries and the ambient air temperature (Figure 15). There are seasonal departures – in the summer water temperature below the confluence is generally higher than either input, and during the winter there are periods when the water is colder. These deviations are in sync with periods of low flows and air temperature extremes. In general, during periods of higher flows, stream temperatures below the confluence are heavily influenced by temperatures of water released to in the creeks from Cherry Reservoir and Lake Eleanor. The LCA project would be operated during the November – March timeframe, which is a relatively non-critical time of year for stream temperatures. Based on these observations, it is expected that increased streamflow in Cherry and Eleanor creeks due to LCA operation would result in smaller deviation from release temperatures during warm and cold days due to the increased thermal mass of the larger volume of water in the stream channel. Figure 15 provides observed temperatures from monitoring locations and the temperatures are all consistent with Sierra Nevada expected stream temperatures, and do not lie outside of the temperature range for the local fishes and other invertebrates. The California Regional Water Quality Control Board, Central Valley Region, Basin Plan (CVRWQCB 2011) sets the following water quality objective for temperature; “At no time or place shall the temperature of COLD or WARM interstate waters be increased more than 5 degrees above natural receiving water temperatures.”. Operation of the LCA project would not result in a temperature increase of more than 5 degrees above natural receiving water temperatures. Operation of LCA would have no impact on temperature in Cherry Lake and Lake Eleanor because water temperatures in Cherry Lake and Lake Eleanor are not expected to vary from historical conditions due to operation of LCA. Operation of LCA would have no impact on temperature in Cherry Creek and Eleanor Creek because releases to the creeks would be made from the reservoirs, which are not expected temperature variation from historical conditions, releases would be made for a short amount of time (up to 4 months), and releases would be made during the November – March timeframe which is a relatively non-critical time of year for stream temperatures.

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Figure 15: Stream temperature at Cherry Creek below Cherry Valley Dam, Eleanor Creek below Eleanor Dam, and Cherry Creek below the Cherry / Eleanor confluence. 7.11 Sediment Transport Effects related to sediment transport can occur in two ways for the LCAER project. The first is sedimentation that could occur as a result of conducting ground disturbing construction activities and stormwater. The second is natural sediment inflow to the creeks and sediment transport as a result of increased flows of up to 200 cfs in sections of the creeks. Each effect of sediment transport is discussed below. 7.11.1 Construction Activities add BMPs Construction activities would create exposed soil from stockpiles, excavated areas, and other ground disturbing activities that could be transported by wind or water, and if not properly managed could increase non-point source sediment loads in receiving water bodies. Increased sediment loads in receiving waters and suspended sediment levels (turbidity) could adversely affect water quality and the designated beneficial uses of surface waters and groundwater. Increased human-caused sediment load to receiving water from construction activities is considered a non-point source of pollution, an environmental indicator. Measures related to this indicator include the amount of ground disturbance, construction stormwater, and erosion/sedimentation. The USFS Water Erosion Prediction Project (WEPP) tool was use to estimate erosion for three locations on the LCAER project; 1) Kelly point staging area, 2 ) canal reach 3, and 3) road & aerial pipe section road. Results are presented in Attachment D. The results in Attachment D are presented for one year (52 weeks) of construction activity. Because construction for LCAER project would be 22 weeks, potential sedimentation results from WEPP are conservative and can be expected to be much less that amounts presented in Attachment D. Site specific Best Management Practices (BMPs) would be applied to the project to reduce non-point source pollution effects to receiving water bodies and wetlands resulting from construction activities from the area of ground disturbance, stormwater, and erosion/sedimentation. BMPs applicable to the project are presented in Attachment C.

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Construction of the LCAER project would not result in impacts to receiving water and wetlands related to non-point source pollution because BMPs presented in Attachment C will be implemented as part of the project construction. 7.11.2 Sediment Transport in Creeks The environmental indicator of Stream Flow includes a measure of sediment transport. This section addresses sediment transport in Cherry and Eleanor creeks. Cherry and Eleanor creek drainages do not have significant sediment transport above the dams as evidenced by the limited sedimentation within the reservoirs. However, the existing dams do limit the potential sediment transport within the river system below. Sediment conditions within the Cherry and Eleanor creek drainages have been and would be greatly impacted by the effects from the Rim Fire. Due to denuding of vegetative soil cover by the fire, increased channel erosion has occurred in areas along the main stream corridor, but primarily along small tributaries. The smaller tributaries have delivered a large quantity of material to the mainstem of Cherry and Eleanor creeks, even during the winter of 2013-14, which experienced very little precipitation. Given the release rates for the LCA and the timing of LCA diversions (November through March), the LCA would increase the rate of transport of sediments, including increased sediment due to the Rim Fire, to the river system during operation of LCA. This material would continue to flow into and be transported and distributed throughout the Tuolumne River system for many years to come. Fine sediments in Cherry and Eleanor creeks below the dams are transported downstream and passed over Cherry Creek Diversion Dam without LCA in operation. With LCA in operation some of the fine sediment would enter LCA and be discharged into Early Intake Reservoir. Most of the fine sediment transported by operation of LCA would be trapped in Early Intake Reservoir. With LCA in operation large sediment, such as gravels and cobble, would collect at Cherry Creek Diversion Dam. Gravel, cobble, and larger sediment would not enter LCA. Some larger sediment would be available to be transported downstream, over Cherry Creek Diversion Dam, with larger flows resulting from wet years, not from LCA operation. Operation of LCA would improve sediment transport in the sections of creek below the dams to the Cherry Creek Diversion Dam due to the increased flow of 200 cfs. Operation of LCA would result in an effect on sediment transport in Cherry and Eleanor Creeks above the Cherry Creek Diversion Dam because of the increase in flow of 200 cfs. Operation of LCA would result in a long term effect to sediment transport downstream of Cherry Creek Diversion Dam because the larger gravel and cobble material transported to Cherry Creek Diversion dam by operation of LCA would be available for transport and distribution throughout the river system for years to come. 7.12 Effects Post LCA Operation The use of the LCA would result in an overall volume loss of up to 48,000 acre-feet of stored water from the Cherry Reservoir and Lake Eleanor system. At the end of the water year in which the LCA would be operated the combined reduction in carry over storage in Cherry Reservoir and Lake Eleanor would be approximately equal to the volume released for LCA diversion. This volume would be recovered in the reservoirs in the years subsequent to LCA operation through natural snowmelt to the reservoirs. The effect of this volume loss and the year in which the recovery would take place would depend on the subsequent hydrologic conditions (i.e. wet or

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dry) but one effect would be lower volumes of water available to release during the recovery year from HPH and Lake Eleanor when compared to no LCA operation. Nonetheless, releases from HPH during the recovery year would be within the range of average annual releases from HPH and releases from Lake Eleanor would meet instream flow requirements. The distribution of the volume loss and change in release amounts would depend on subsequent hydrology. Under historic conditions, cumulative release volumes below facilities have varied greatly depending on hydrologic conditions. The greatest variance in flow volumes within the Cherry Creek system is below HPH (Figure 16). Figure 16 shows a statistical representation of historic releases from HPH during the period of 1993 – 2014. The shaded box on the left side of Figure 16 indicates the range of releases for 90 percent of the data set. The lines that extend up and down from the shaded box indicate release amounts outside of 90 percent of the data set. Figure 16 shows a statistical representation of historic releases from HPH during the period of 1993 – 2014 by year. If conditions are wet, a large volume of water can be released as shown in 1995 and 1997 on Figure 16 release from HPH can be above 500,000 acre feet. In drier years or in years following lowering for maintenance such as 2001, 2008, and 2012 releases from HPH are closer to 175,000 – 200,000 acre feet. In order to provide context of the change in distribution and reduction in stored water due to LCA operations, an analysis was performed using current system storage conditions of three dry years in a row under three hydrologic recovery scenarios: extended dry conditions, a return to normal conditions and wet conditions (Table 5). These scenarios assume current conditions of three dry years in a row and use a Year 1 of extremely dry conditions with LCA in use for four months and compares releases resulting from LCA operations to releases when LCA is not in use. The analysis assumes 2014 end of year conditions prior to the operation of LCA in Year 1. For all scenarios Year 1 has the hydrologic condition of the 1977 water year, the driest year on record. This assumption creates a drought scenario that is worse than any condition in the historic record. With the assumption of a 2014 water year flowed by a 1977 water year and operating under Water First Policy, releases from HPH are reduced through the persistence of the drought period. If the current extreme drought conditions continue, releases from HPH are expected to be approximately 36,000 – 38,000 acre feet irrespective of whether LCA is in operation. This release volume would contribute to meet downstream flow obligations to the districts. The years following Year 1 are different hydrologic years to create the three hydrologic recovery scenarios: extended dry conditions, a return to normal conditions and wet conditions. The extended dry condition scenario is equivalent to a six year drought. The system is then operated to meet operational restrictions, instream flow requirements, flow obligations to the districts, and to manage reservoir elevations. This assessment shows that the volume impact is observed in a single year (either the second or third year after LCA is operated, depending on hydrological conditions). Once the system reaches capacity it has recovered from any potential release impacts of LCA operations. In the dry hydrological sequence scenario, the result of the use of LCA is lower releases through HPH in the third year following a 4-month period of LCA use. Without LCA in operation releases below HPH would be approximately 300,000 acre feet in the third year. With LCA in operation the releases below HPH would be approximately 247,000 acre feet, a reduction of 53,000 acre feet. Releases below HPH in year three when the lost storage is being recovered and releases are reduced due to the storage recovery, are within the range of historic operations as shown on Figure 16. The storage is recovered and the system reaches capacity during Year 4.

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In a normal hydrological sequence scenario, the year following LCA use (Year 2) has lower releases from HPH and then recovers in the third year. Without LCA in operation releases below HPH would be approximately 360,000 acre feet in Year 2. With LCA in operation the releases below HPH would be approximately 315,000 acre feet, a reduction of 44,000 acre feet. Releases below HPH in Year 2 when the lost storage is being recovered and releases are reduced due to the storage recovery, are within the range of historical operations as shown on Figure 16. The storage is recovered and the system reaches capacity in Year 4. In the wet scenario, release volumes are reduced from Lake Eleanor, Cherry Reservoir, and HPH in Year 2. Without LCA in operation releases below HPH would be approximately 521,000 acre feet in Year 2. With LCA in operation the releases below HPH would be approximately 501,000 acre feet, a reduction of 20,000 acre feet. Releases from Eleanor and Cherry are also reduced by approximately 25, 000 acre feet. Releases below HPH in Year 2 when the lost storage is being recovered and releases are reduced due to the storage recovery, are within the range of historical operations as shown on Figure 16. The storage is recovered and the system reaches capacity at the end of Year 2.

Figure 16: Distribution of historic annual flow volumes from HPH during the 1993 through 2014 period. Distribution reflects normal operations and does not account for times of severe drought.

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Table 5. Total release volumes (in thousand acre-feet) below each facility three hydrologic recovery scenarios under LCA use and no LCA use condition in Year 1. 7.13 Cumulative Past, current, and foreseeable future projects identified in chapter 3, table 3.1-1 were reviewed to determine if they contributed or could contribute to water quality and soils effects when considered in combination with the LCAER project. Three projects, 1) Emergency Hazard Tree Removal along Cherry Lake Road, all powerlines and LCA open canal segments (past project), 2) Rim Fire Recovery (Record of Decision, USDA 2014a) (future project), and 3) Rim Fire Reforestation (future project), have the potential to affect soils and water resources through actions that may cause erosion and sedimentation. The Rim Fire and associated recovery actions included in the past and future projects have made, and will continue to make, the greatest contribution to cumulative impacts related to erosion and sedimentation in the proposed action area. The Rim Fire Recovery project would include timber salvage on about 15,000 acres and hazard tree removal on about 17,000 acres. The Emergency Hazard Tree Removal included timber salvage in areas along Cherry Creek Road and LCA open canal segments. Rim Fire Reforestation would include site preparation and planting of up to 30,000 acres. Ground disturbance associated with these projects could contribute to cumulative effects related to water quality and soils. BMPs, such as stormwater controls, would be included in the projects to minimize effects on water quality and soils resulting from potential erosion and sedimentation. The proposed action includes extensive BMPs to minimize the potential for construction activity in the small (less than 20 acres) construction area to result in erosion, sedimentation, or non-point source pollution. With these BMPs in place, the proposed action would make a negligible contribution towards cumulative erosion and sedimentation impacts. The incremental

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contribution of the proposed action to the overall cumulative effects of erosion and sedimentation is negligible. The Forest Service in Region 5 has adopted the Equivalent Roaded Acres (ERA) model as a method of addressing cumulative watershed effects. This model is designed as a preliminary indicator for managers to determine whether or not past and present land management disturbances in a given watershed approach or exceed a threshold of concern (TOC). Where ERAs approach or exceed a given watershed’s TOC, further field work would be necessary to ascertain whether cumulative watershed effects are present and if land management activities would adversely add to those effects and result in detrimental impacts to beneficial uses. The ERA model develops an ERA coefficient for each type of disturbance based on the nature of the disturbance and recovery times associated with those disturbances. A TOC is then developed for each watershed to determine the type and amount of development that could take place within the watershed without exceeding the TOC. The LCAER project would not convert undeveloped land to developed land. All work for the LCAER project would take place on existing graded staging areas, existing roads, and existing water system, resulting in an ERA rating of zero. The LCAER project ERA of 0 would not contribute to exceeding the TOC for the Lower Cherry Creek HUC level 6 watershed. No other past, present or reasonably foreseeable future projects would contribute to the effects of operation of the LCA with respect to reservoirs and streams. The effects of LCA operation were in any case assessed as within the historical operating range of HHWP reservoirs and related stream flows. 8. No Action Alternative Under the no action alternative the LCA would be operated at 165 cfs (delivering 40,000 af of stored water over a four-month period).

Only minor construction activities, including periodic maintenance and installation of bat gates, would occur, although replacement of headgates, sluice gates, and elevated segments of pipeline likely would be needed in the future to maintain the reliability of the system. Potential environmental effects associated with construction of the LCAER project would not occur. Because little or no ground disturbance would occur, the no action alternative would have less potential than the proposed action to result in erosion or in water quality effects and associated with construction runoff. Less ground disturbance would occur along the CCDD access path and near the aerial pipeline, where wetlands are present; however, these also would be avoided under the proposed action.

Under this alternative streamflow, reservoir elevation, water temperature and sediment transport effects related to LCA operation would be slightly reduced when compared to the proposed action because the no action alternative would use 8,000 fewer acre-feet of the stored reservoir water, such that reservoir storage would recover slightly more quickly. As under the proposed action, during the recovery periods, stored water volumes are expected to be sufficient to support releases at the full capacity of HPH for at least four hours daily during the summer months, as under existing conditions.

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As illustrated by table 3.2-6, below, minimum instream flows in each of the creeks would be maintained irrespective of the operation of the LCA.

Table 6. Instream Flows with Operation of No Action (in Cubic Feet per Second)

Nov-Dec Jan-Mar

Eleanor Creek Minimum Instream flow 5 5 LCA release to Eleanor Creek 165 Total flow in Eleanor Creek 170 5

Cherry Creek minimum instream flow 5 5

LCA release to Cherry Creek 165 Total flow in Cherry Creek upstream of confluence 5 170 Total flow in Cherry Creek downstream of confluence 10 175

The 35 cfs difference in flow rate and 8,000 af difference in water storage volume under the no action alternative as compared with the proposed action is within the range of error in hydrologic modeling for the system and would not be anticipated to result in a noticeable difference in streamflows, sediment transport or reservoir fluctuations. 9. Summary of Effects Use of the LCA would allow the HHRWS to deliver water stored in Lake Eleanor and Cherry Reservoir to the Bay Area during periods of extended drought emergency, consistent with past use of the facility. Use of the LCA system is operationally restricted to approximately four months, which would result in the diversion of about 48,000 acre-feet in total from Lake Eleanor and Cherry Reservoir. Releases for LCA diversion would initially be made from Lake Eleanor into Eleanor Creek followed by release from Cherry Reservoir into Cherry Creek. Releases from the reservoirs would result in increased flows in Cherry Creek and Eleanor Creek upstream of the Cherry Creek Diversion Dam during the period of LCA operation as compared with those that typically occur during these months under the existing conditions during drought and non-drought years. However the estimated maximum release rate of 200 cfs is within the annual bounds of the existing flow regime currently in place as well as the calculated flow regime assuming no dams and reservoirs on the creeks. Diversions to the LCA would result in lower storage levels in Cherry Reservoir as drought conditions continue. The reservoir level may be 6 to 30 feet lower than under baseline conditions depending on the duration of LCA diversions and hydrological conditions in a given year. The lower water elevation in Cherry Reservoir that would result from LCA operations is within the range experienced during normal operations and maintenance. Operation of the LCA does not impact the seasonal elevation at Lake Eleanor. Reservoir water temperature is the controlling factor of water temperature within the Cherry Creek drainage. During low flow periods, the meteorological conditions can result in a departure to colder or warmer conditions. An increase in flow would buffer daily variation in water

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temperature in the creeks, but the overall temperature regime would remain near the current condition. Water temperature in the reservoirs is anticipated to remain near the current conditions. Releases for LCA operations would increase the sediment transport in Cherry and Eleanor creeks to the Cherry Creek Diversion Dam. Fine sediments would enter LCA and be trapped in Early Intake Reservoir. Larger material, such as gravel and cobble, would be deposited at Cherry Creek Diversion Dam and would be available for transport downstream during large flow events. Given the dampening effects of the reservoirs on streamflow, and the generally sediment starved nature of the downstream reaches, the increased sediment transport and available material is expected to be beneficial to stream health. The diversion of water to the LCA results in a lower storage volume within the Cherry Reservoir and Lake Eleanor system. When the hydrologic conditions recover there would be less water available for release within the Cherry Reservoir and Lake Eleanor system approximately equal to the volume diverted through the LCA. Under a four month scenario of LCA operations at a rate of 200 cfs, there is approximately 48,000 acre-feet less release. This volume represents 7 to 22% of the total release volume during hydrologic recovery. 10. Compliance with Forest Plan and Other Direction Attachment A lists Stanislaus National Forest, Forest Plan Direction (Forest Plan) (USDA 2010) Standards and Guidelines (S&Gs) applicable to watershed resources, as well as how the S&Gs would be met. Attachment A also identifies Forest Plan Land Allocation areas and associated standards and guidelines. The LCAER project complies with the Stanislaus Forest Plan because construction of the project complies with all applicable Federal and State water quality standards, water quality BMPs for protection of non-point water pollution sources will be implemented, and beneficial uses of water bodies are protected and not affected by the project. 10.1 Beneficial Uses of Water The project is expected to result in maintenance of the applicable beneficial uses of water in the Water Quality Control Plan (Basin Plan) for the California Central Valley Water Quality Control Board (CVRWQCB 2011). Water temperature, sediment, and water quality are not expected to be adversely altered as a result of construction or operation of the LCA project. Beneficial uses of irrigation; stock watering; contact; other non-contact; warm; cold; and wildlife habitat are not expected to be adversely altered as a result of construction or operation of the LCA project. Beneficial use of power and canoeing and rafting would continue to be maintained; however, may be reduced as a result of LCA operations in the one year of recovery, however would be within the historic range. Due to operation of LCA during droughts, less water is available for power generation and shaping releases for rafting when compared to wet years. Beneficial use of municipal and domestic supply is expected to be maintained. 10.2 Water Quality Best Management Practices (BMPs) The LCA project complies with the intent and procedural requirements of BMPs ( USDA 2012). BMPs applicable to the LCA project are identified in Attachment C. 11. References (CVRWQCB 2011) California Regional Water Quality Control Board, Central Valley Region. 2011. The water quality control plan (Basin Plan) for the California Regional

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Water Quality Control Board, Central Valley Region: The Sacramento River Basin Plan and the San Joaquin River Basin. 4th ed., rev. Sacramento, CA. II-8.00p. (USDA 1998) USDA Forest Service, Stanislaus National Forest. 1988 (reprint 2002). USDA Forest Service, Stanislaus National Forest Tuolumne Wild and Scenic River Management Plan. (USDA 2007) USDA Forest Service. 2007. USDA Forest Service Strategic Plan: 2007 – 2012. USDA Forest Service. FS-880. 38p. (USDA 2010) USDA Forest Service, Stanislaus National Forest. 2010. USDA Forest Service, Stanislaus National Forest, Forest Plan Direction. (USDA 2012) USDA Forest Service 2012 National Best Management Practices for Water Quality Management on National Forest System Lands, Volume 1 – National Core BMP Technical Guide. FS-990a. Washington, DC. April. Available at: http://www.fs.fed.us/biology/resources/pubs/watershed/FS_National_Core_BMPs_April2012.pdf (USGS 2013) USGS. 2013. Federal Standards and Procedures for the National Watershed Boundary Dataset (WBD) (4 ed.): Techniques and Methods 11-A3, 63p.

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Attachment A

Attachment A1 Stanislaus National Forest, Forest Plan Direction April 2010 Forestwide Standards and Guidelines – Water

Practices General Direction Standards and Guidelines Water Quality Management (18-A)

Comply with all applicable Federal and State water quality standards. Prevent or minimize as much as possible any water quality impacts which may be caused by Forest management activities. Achieve the goals for preventing or minimizing water pollution as stated in the Federal Clean Water Act. Implement water quality Best Management Practices (BMPs) as specified in the Management Agency Agreement with the California Water Resources Control Board for protection of non-point water pollution sources. Comply with applicable provisions of the Water Quality Control Plan (Basin Plan) of the California Central Valley Regional Water Control Board.

Implement water quality Best Management Practices (BMPs) as needed for all Forest management activities. BMPs are a system of nearly 100 practices designed to minimize or prevent water pollution from Forest management activities. They cover such activities as timber harvest, road construction, mining, recreation, fire management and grazing. See Appendix K of the EIS for a discussion and listing of the water quality BMPs. Monitor the implementation and effectiveness of BMPs in selected areas to determine if they are being carried out and if they are accomplishing their objectives. Analyze cumulative watershed effects (CWE) on all applicable proposed Forest management activities to determine off-site effects on the beneficial uses of water.

Water Quantity Management (18- B)

Support water yield increase where economically feasible and environ- mentally acceptable. Follow Forest Service Manual policy for proposed weather modification projects, especially in designated Wilderness. Provide input to proposals for water supply and hydroelectricity which may alter fluvial systems by construction of facilities such as dams, diversions and tunnels. Such input will support valid proposals provided they are consistent with sound watershed resource protection measures. Support all valid uses of water from the National Forest. Insure that such uses are carried out commensurate with Federal and State laws and regulations.

Follow all Federal and State regulatory practices required in responding to proposals to develop the water resource. Keep current all water rights management for beneficial uses of water on the Forest.

Watershed Maintenance and Improvement (18-D)

Maintain or improve watershed condition to provide stewardship of water and soil resources. Survey Forest watersheds and restore degraded areas to improve watershed condition. Establish a Forestwide water resources inventory (WRI) to determine needs for maintenance and improvement of the water resource. The WRI is a comprehensive data base of water resource information for each Forest watershed. It is used to determine watershed condition to (1) protect or enhance the water resource when planning forest management activities and (2) to determine watershed improvement needs (WIN).

Conduct periodic watershed surveys to determine the current condition of the water resource, identify potential WIN projects and assess the potential for cumulative watershed effects. Conduct disaster surveys as needed and prescribe applicable emergency rehabilitation treatments. Such disasters include wildfires, floods, earthquakes and damage from high winds and avalanches. Implement the following watershed recovery practices following major wildfires, except in Wilderness in most cases: 1. Restore ground cover as soon as possible when

necessary to reduce flood flows to protect life and property, to maintain soil productivity and/or to minimize stream sedimentation and cumulative watershed effects.

2. Conduct reforestation activities in a manner which reduces the potential for cumulative watershed effects, such as dispersing site preparation adequately over time and space and/or using techniques which minimize land disturbance.

Attachment A2 Stanislaus National Forest, Forest Plan Direction April 2010 Riparian Conservation Areas

Riparian Conservation Areas

Designation Riparian Conservation Area (RCA) widths are described below. RCA widths may be adjusted at the project level if a landscape analysis has been completed and a site-specific Riparian Conservation Objectives (RCO) analysis demonstrates a need for different widths. Perennial Streams: 300 feet on each side of the stream, measured from the bank full edge of the stream. Seasonally Flowing Streams (includes intermittent and ephemeral streams): 150 feet on each side of the stream, measured from the bank full edge of the stream.

Streams in Inner Gorge1: top of inner gorge.

Special Aquatic Features2 or Perennial Streams with Riparian Conditions extending more than 150 feet from edge of streambank or Seasonally Flowing streams with riparian conditions extending more than 50 feet from edge of streambank: 300 feet from edge of feature or riparian vegetation, whichever width is greater. Other hydrological or topographic depressions without a defined channel: RCA width and protection measures determined through project level analysis.

Desired Conditions Water quality meets the goals of the Clean Water Act and Safe Drinking Water Act; it is fishable, swimmable, and suitable for drinking after normal treatment.

Habitat supports viable populations of native and desired non-native plant, invertebrate, and vertebrate riparian and aquatic-dependent species. New introductions of invasive species are prevented. Where invasive species are adversely affecting the viability of native species, the appropriate State and Federal wildlife agencies have reduced impacts to native populations.

Species composition and structural diversity of plant and animal communities in riparian areas, wetlands, and meadows provide desired habitat conditions and ecological functions.

1 Inner gorge is defined by stream adjacent slopes greater than 70 percent gradient 2 Special Aquatic Features include: lakes, wet meadows, bogs, fens, wetlands, vernal pools, and springs

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The distribution and health of biotic communities in special aquatic habitats (such as springs, seeps, vernal pools, fens, bogs, and marshes) perpetuates their unique functions and biological diversity.

Spatial and temporal connectivity for riparian and aquatic-dependent species within and between watersheds provides physically, chemically and biologically unobstructed movement for their survival, migration and reproduction.

The connections of floodplains, channels, and water tables distribute flood flows and sustain diverse habitats.

Soils with favorable infiltration characteristics and diverse vegetative cover absorb and filter precipitation and sustain favorable conditions of stream flows.

In-stream flows are sufficient to sustain desired conditions of riparian, aquatic, wetland, and meadow habitats and keep sediment regimes as close as possible to those with which aquatic and riparian biota evolved.

The physical structure and condition of stream banks and shorelines minimizes erosion and sustains desired habitat diversity.

The ecological status of meadow vegetation is late seral (50 percent or more of the relative cover of the herbaceous layer is late seral with high similarity to the potential natural community). A diversity of age classes of hardwood shrubs is present and regeneration is occurring.

Meadows are hydrologically functional. Sites of accelerated erosion, such as gullies and headcuts are stabilized or recovering. Vegetation roots occur throughout the available soil profile. Meadows with perennial and intermittent streams have the following characteristics: (1) stream energy from high flows is dissipated, reducing erosion and improving water quality, (2) streams filter sediment and capture bedload, aiding floodplain development, (3) meadow conditions enhance floodwater retention and groundwater recharge, and (4) root masses stabilize stream banks against cutting action.

Standards and Guidelines Designate riparian conservation area (RCA) widths as described above. The RCA widths displayed may be adjusted at the project level if a landscape analysis has been completed and a site-specific RCO analysis demonstrates a need for different widths.

Evaluate new proposed management activities within CARs and RCAs during environmental analysis to determine consistency with the riparian conservation objectives at the project level and the AMS goals for the landscape. Ensure that appropriate mitigation measures are enacted to (1) minimize the risk of activity-related sediment entering aquatic systems and (2) minimize impacts to habitat for aquatic- or riparian-dependent plant and animal species.

Identify existing uses and activities in CARs and RCAs during landscape analysis. At the time of permit reissuance, evaluate and consider actions needed for consistency with RCOs.

As part of project-level analysis, conduct peer reviews for projects that propose ground-disturbing activities in more than 25 percent of the RCA or more than 15 percent of a CAR.

192 Forest Plan Direction April 2010

Attachment A2 Stanislaus National Forest, Forest Plan Direction April 2010 Riparian Conservation Areas

RCO Standards and Guidelines Riparian Conservation Objective 1: Ensure that identified beneficial uses for the water body are adequately protected. Identify the specific beneficial uses for the project area, water quality goals from the Regional Basin Plan, and the manner in which the standards and guidelines will protect the beneficial uses.

For waters designated as “Water Quality Limited” (Clean Water Act Section 303(d)), participate in the development of Total Maximum Daily Loads (TMDLs) and TMDL Implementation Plans. Execute applicable elements of completed TMDL Implementation Plans. Ensure that management activities do not adversely affect water temperatures necessary for local aquatic- and riparian-dependent species assemblages. Limit pesticide applications to cases where project level analysis indicates that pesticide applications are consistent with riparian conservation objectives. Within 500 feet of known occupied sites for the California red-legged frog, Cascades frog, Yosemite toad, foothill yellow-legged frog, mountain yellow-legged frog, and northern leopard frog, design pesticide applications to avoid adverse effects to individuals and their habitats. Prohibit storage of fuels and other toxic materials within RCAs and CARs except at designated administrative sites and sites covered by a Special Use Authorization. Prohibit refueling within RCAs and CARs unless there are no other alternatives. Ensure that spill plans are reviewed and up-to-date.

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Riparian Conservation Objective 2: Maintain or restore: (1) the geomorphic and biological characteristics of special aquatic features, including lakes, meadows, bogs, fens, wetlands, vernal pools, springs; (2) streams, including in stream flows; and (3) hydrologic connectivity both within and between watersheds to provide for the habitat needs of aquatic-dependent species.

Maintain and restore the hydrologic connectivity of streams, meadows, wetlands, and other special aquatic features by identifying roads and trails that intercept, divert, or disrupt natural surface and subsurface water flow paths. Implement corrective actions where necessary to restore connectivity. Ensure that culverts or other stream crossings do not create barriers to upstream or downstream passage for aquatic-dependent species. Locate water drafting sites to avoid adverse effects to in stream flows and depletion of pool habitat. Where possible, maintain and restore the timing, variability, and duration of floodplain inundation and water table elevation in meadows, wetlands, and other special aquatic features. Prior to activities that could adversely affect streams, determine if relevant stream characteristics are within the range of natural variability. If characteristics are outside the range of natural variability, implement mitigation measures and short-term restoration actions needed to prevent further declines or cause an upward trend in conditions. Evaluate required long-term restoration actions and implement them according to their status among other restoration needs. Prevent disturbance to streambanks and natural lake and pond shorelines caused by resource activities (for example, livestock, off-highway vehicles, and dispersed recreation) from exceeding 20 percent of stream reach or 20 percent of natural lake and pond shorelines. Disturbance includes bank sloughing, chiseling, trampling, and other means of exposing bare soil or cutting plant roots. This standard does not apply to developed recreation sites, sites authorized under Special Use Permits and designated off-highway vehicle routes. In stream reaches occupied by, or identified as “essential habitat” in the conservation assessment for, the Lahonton and Paiute cutthroat trout and the Little Kern golden trout, limit streambank disturbance from livestock to 10 percent of the occupied or “essential habitat” stream reach. Cooperate with State and Federal agencies to develop streambank disturbance standards for threatened, endangered, and sensitive species. Use the regional streambank assessment protocol. Implement corrective action where disturbance limits have been exceeded. At either the landscape or project-scale, determine if the age class, structural diversity, composition, and cover of riparian vegetation are within the range of natural variability for the vegetative community. If conditions are outside the range of natural variability, consider implementing mitigation and/or restoration actions that will result in an upward trend. Actions could include restoration of aspen or other riparian vegetation where conifer encroachment is identified as a problem. Cooperate with Federal, Tribal, State and local governments to secure in stream flows needed to maintain, recover, and restore riparian resources, channel conditions, and aquatic habitat. Maintain in stream flows to protect aquatic systems to which species are uniquely adapted. Minimize the effects of stream diversions or other flow modifications from hydroelectric projects on threatened, endangered, and sensitive species. For exempt hydroelectric facilities on national forest lands, ensure that special use permit language provides adequate in stream flow requirements to maintain, restore, or recover favorable ecological conditions for local riparian- and aquatic-dependent species.

194 Forest Plan Direction April 2010

Attachment A2 Stanislaus National Forest, Forest Plan Direction April 2010 Riparian Conservation Areas

RCO Standards and Guidelines Riparian Conservation Objective 3: Ensure a renewable supply of large down logs that: (1) can reach the stream channel and (2) provide suitable habitat within and adjacent to the RCA.

Determine if the level of coarse large woody debris (CWD) is within the range of natural variability in terms of frequency and distribution and is sufficient to sustain stream channel physical complexity and stability. Ensure proposed management activities move conditions toward the range of natural variability.

Riparian Conservation Objective 4: Ensure that management activities, including fuels reduction actions, within RCAs and CARs enhance or maintain physical and biological characteristics associated with aquatic- and riparian- dependent species.

Within CARs, in occupied habitat or “essential habitat” as identified in conservation assessments for threatened, endangered, or sensitive species, evaluate the appropriate role, timing, and extent of prescribed fire. Avoid direct lighting within riparian vegetation; prescribed fires may back into riparian vegetation areas. Develop mitigation measures to avoid impacts to these species whenever ground-disturbing equipment is used. Use screening devices for water drafting pumps. (Fire suppression activities are exempt during initial attack.) Use pumps with low entry velocity to minimize removal of aquatic species, including juvenile fish, amphibian egg masses and tadpoles, from aquatic habitats. Design prescribed fire treatments to minimize disturbance of ground cover and riparian vegetation in RCAs. In burn plans for project areas that include, or are adjacent to RCAs, identify mitigation measures to minimize the spread of fire into riparian vegetation. In determining which mitigation measures to adopt, weigh the potential harm of mitigation measures, for example fire lines, against the risks and benefits of prescribed fire entering riparian vegetation. Strategies should recognize the role of fire in ecosystem function and identify those instances where fire suppression or fuel management actions could be damaging to habitat or long-term function of the riparian community. Post-wildfire management activities in RCAs and CARs should emphasize enhancing native vegetation cover, stabilizing channels by non-structural means, minimizing adverse effects from the existing road network, and carrying out activities identified in landscape analyses. Post-wildfire operations shall minimize the exposure of bare soil. Allow hazard tree removal within RCAs or CARs. Allow mechanical ground disturbing fuels treatments, salvage harvest, or commercial fuelwood cutting within RCAs or CARs when the activity is consistent with RCOs. Utilize low ground pressure equipment, helicopters, over the snow logging, or other non-ground disturbing actions to operate off of existing roads when needed to achieve RCOs. Ensure that existing roads, landings, and skid trails meet Best Management Practices. Minimize the construction of new skid trails or roads for access into RCAs for fuel treatments, salvage harvest, commercial fuelwood cutting, or hazard tree removal. As appropriate, assess and document aquatic conditions following the Regional Stream Condition Inventory protocol prior to implementing ground disturbing activities within suitable habitat for California red-legged frog, Cascades frog, Yosemite toad, foothill and mountain yellow-legged frogs, and northern leopard frog. During fire suppression activities, consider impacts to aquatic- and riparian-dependent resources. Where possible, locate incident bases, camps, helibases, staging areas, helispots, and other centers for incident activities outside of RCAs or CARs. During pre-suppression planning, determine guidelines for suppression activities, including avoidance of potential adverse effects to aquatic- and riparian-dependent species as a goal. Identify roads, trails, OHV trails and staging areas, developed recreation sites, dispersed campgrounds, special use permits, grazing permits, and day use sites during landscape analysis. Identify conditions that degrade water quality or habitat for aquatic and riparian-dependent species. At the project level, evaluate and consider actions to ensure consistency with standards and guidelines or desired conditions.

195

RCO Standards and Guidelines Riparian Conservation Objective 5: Preserve, restore, or enhance special aquatic features, such as meadows, lakes, ponds, bogs, fens, and wetlands, to provide the ecological conditions and processes needed to recover or enhance the viability of species that rely on these areas.

Assess the hydrologic function of meadow habitats and other special aquatic features during range management analysis. Ensure that characteristics of special features are, at a minimum, at Proper Functioning Condition, as defined in the appropriate Technical Reports (or their successor publications): (1) “Process for Assessing PFC” TR 1737-9 (1993), “PFC for Lotic Areas” USDI TR 1737-15 (1998) or (2) “PFC for Lentic Riparian-Wetland Areas” USDI TR 1737-11 (1994). Prohibit or mitigate ground-disturbing activities that adversely affect hydrologic processes that maintain water flow, water quality, or water temperature critical to sustaining bog and fen ecosystems and plant species that depend on these ecosystems. During project analysis, survey, map, and develop measures to protect bogs and fens from such activities as trampling by livestock, pack stock, humans, and wheeled vehicles. Criteria for defining bogs and fens include, but are not limited to, presence of: (1) sphagnum moss (Spagnum spp.), (2) mosses belonging to the genus Meessia, and (3) sundew (Drosera spp.) Complete initial plant inventories of bogs and fens within active grazing allotments prior to re-issuing permits. Locate new facilities for gathering livestock and pack stock outside of meadows and riparian conservation areas. During project-level planning, evaluate and consider relocating existing livestock facilities outside of meadows and riparian areas. Prior to re-issuing grazing permits, assess the compatibility of livestock management facilities located in riparian conservation areas with riparian conservation objectives. Under season-long grazing: For meadows in early seral status: limit livestock utilization of grass and grass-like plants to 30

percent (or minimum 6-inch stubble height). For meadows in late seral status: limit livestock utilization of grass and grass-like plants to a

maximum of 40 percent (or minimum 4-inch stubble height). Determine ecological status on all key areas monitored for grazing utilization prior to establishing utilization levels. Use Regional ecological scorecards and range plant list in regional range handbooks to determine ecological status. Analyze meadow ecological status every 3 to 5 years. If meadow ecological status is determined to be moving in a downward trend, modify or suspend grazing. Include ecological status data in a spatially explicit Geographical Information System database. Under intensive grazing systems (such as rest-rotation and deferred rotation) where meadows are receiving a period of rest, utilization levels can be higher than the levels described above if the meadow is maintained in late seral status and meadow-associated species are not being impacted. Degraded meadows (such as those in early seral status with greater than 10 percent of the meadow area in bare soil and active erosion) require total rest from grazing until they have recovered and have moved to mid- or late seral status. Limit browsing to no more than 20 percent of the annual leader growth of mature riparian shrubs and no more than 20 percent of individual seedlings. Remove livestock from any area of an allotment when browsing indicates a change in livestock preference from grazing herbaceous vegetation to browsing woody riparian vegetation.

Riparian Conservation Objective 6: Identify and implement restoration actions to maintain, restore or enhance water quality and maintain, restore, or enhance habitat for riparian and aquatic species.

Recommend restoration practices in: (1) areas with compaction in excess of soil quality standards, (2) areas with lowered water tables, or (3) areas that are either actively down cutting or that have historic gullies. Identify other management practices, for example, road building, recreational use, grazing, and timber harvests that may be contributing to the observed degradation.

196 Forest Plan Direction April 2010

Attachment B

Upper Tuolumne River:

Description of River Ecosystem and Recommended Monitoring Actions

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Upper Tuolumne River: Description of River Ecosystem Chapter 6 Synthesis of Available Information and Recommended Monitoring Actions

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Chapter 6 Synthesis of Available Information

Technical Memorandum #2 prepared by McBain & Trush and R M C Water and Environment summarized existing available information collected to date. Additional field observations were made in spring and summer 2006 focusing on the high flow releases provided by the S F P U C and natural high flows provided by the Extremely Wet water year. This section synthesizes existing available information with our 2006 field observations to refine hypotheses about how the river ecosystem historically functioned and how it change in order to guide additional monitoring priorities (Section 7), and eventually developing recommendations for operational adjustment to improve ecosystem function. The following section focuses on stream geomorphology, riparian vegetation, and priority analysis species (fish, amphibians, benthic macroinvertebrates, etc).

6.1 Eleanor Creek

6.1.1 G e o m o r p h o l o g y

Sources of geomorphic information on Eleanor Creek are few. The primary geomorphic information sources are USGS topographic maps, U S G S digital elevation model (DEM), and our 2006 field reconnaissance. The best quantitative information that provides insights to Eleanor Creek geomorphology is long-term U S G S flow data at the Eleanor Creek near Hetch Hetchy gaging station (USGS 11-278000).

Based on our field reconnaissance and the U S G S 10 meter grid D E M , a general overview of Eleanor Creek geomorphology was developed. First, glaciers during the Tioga glaciation (approximately 10,000 years ago) likely extended downstream to the confluence of Cherry Creek, resulting in extensive exposed granite, shallow soils, and sparse forested land above Lake Eleanor. Second, a pronounced feature of the Eleanor Creek profile (and most other streams draining the west side of the Sierra Nevada) is the nick point where the rapid incision of the streams into the uplifting Sierra Nevada range tapers off (Figure 6-1). The morphology of the valley and the stream is markedly different upstream and downstream of this transition. On Eleanor Creek, this location is approximately % mile downstream of Eleanor Dam. Upstream of the nick point, the valley has been frequently glaciated, is broader and less confined, has shallow soils and exposed granitic bedrock, and is moderate gradient (2% to 3%). The dominant sediment delivery mechanism to the creek is granite block exfoliation and decomposed granitic sand delivery from wind and surface water flow. The stream channel morphology is largely shaped by historic glaciation rather than the stream itself: there are periodic lower gradient reaches separated by steep cascades over steep bedrock drops, as is observed at the Eleanor Dam site (Figure 6-2) and likely numerous other locations upstream. However, none of these glaciated bedrock drops were observed downstream of the dam site. The substrate upstream of the nick point is largely exposed granite bedrock and locally derived boulders, with some pockets of cobbles, gravel, and sand (Figure 6-3).

Downstream of the nick point, the channel morphology is largely dictated by fluvial processes of the stream itself, and less so than glacial processes. The channel is incised within the uplifting Sierra Nevada bedrock, is much steeper (>6%), and very confined by the valley walls. The dominant sediment delivery mechanism to the creek is landslides and rockfalls of fractured granitic blocks from the valley walls. Fires and timber management are very frequent downstream of Eleanor Dam, which likely increases fine sediment contribution to the stream. The steep confined channel easily transports fine sediment downstream, largely masking any morphologic response to this potential increase in fine sediment supply. The bed surface is typically a thin layer of large boulders on top of bedrock (Figure 6-4). There are several falls/cascades that create large pools downstream (Figure 6-5).

As described in Section 5, low magnitude floods in the 1.5 to 2.3-year flood recurrence have been substantially reduced, while the larger, less frequent floods greater than 5-year recurrence have been less impacted by flow regulation from Lake Eleanor. Therefore, bed mobility still occurs, but likely less frequently than pre-dam conditions. Based on our field reconnaissance, the frequency of high flows has

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remained sufficient to prevent riparian or upland vegetation encroachment into the low flow channel, and there does not appear to have been any morphologic effect on the channel from riparian vegetation encroachment (in contrast to Cherry Creek). Additionally, because Eleanor Dam is simply an enlarged natural lake, the sediment supply from the upper watershed was always trapped, thus the sediment supply to the project reach immediately downstream of Eleanor Dam has not changed. Lastly, during large floods, water and large wood appear to flow over the top of the dam, such that change in large wood supply to downstream reaches due to Eleanor Dam is likely small. Large wood accumulations were observed at several locations downstream of the dam (Figure 6-6). The net result is that the Eleanor Creek geomorphology appears to be functioning similarly to unregulated streams regionally.

Figure 6-1: Eleanor Creek Profile from USGS 10 m Digital Elevation Model Showing Increase in Channel Gradient % mile Downstream of Eleanor Dam.

5,000

4,800

4,600 I

D 4,400 + > < z £ 4,200 c o a ra J> 4,000 UJ

3,800

3,600 f

3,400

Lake Eleanor

GradiBDt_=3J3fj%

Cherry Creek

Confluence

-+-

570000 575000 580000 585000 590000

Feet Upstream from Confluence of San Joaquin River

595000

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Figure 6-2: Eleanor Creek Looking Downstream from Eleanor Dam, Illustrating Steep Bedrock Drop Followed by Moderate Gradient, Less Confined Reach.

Figure 6-3: Eleanor Creek Looking Upstream and Downstream near USGS Gaging Station Vt mile Downstream of Eleanor Dam, Illustrating Exposed Granite Bedrock Channel Bed with Granite

Boulders (left photo) with Cobble/Gravel/Sand Pockets (right photo).

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Figure 6-4: Lower Eleanor Creek Showing Valley Confinement, Steep Gradient, and Boulder Bed.

Figure 6-5: Large Pool at Top of Lower Eleanor Creek Canyon.

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Figure 6-6:1997 Flood Debris (19,500 cfs) at Eleanor Creek near Hetch Hetchy Gaging Station (USGS 11-278000) Approximately 20 ft Above Low Flow Water Surface (Left Photo), and 2005

Flood Debris (7,400 cfs) Downstream 1 Mile (Right Photo), Showing that Eleanor Creek Floods Move Entire Trees, Boulders, and Cobbles.

6.1.2 Water Temperature

Of all the reservoirs operated by the SFPUC, Lake Eleanor has likely caused the fewest changes to the downstream water temperature regime in Eleanor Creek. Under natural conditions, water temperatures in the stream were dictated by water temperatures in the epilimnion of the pre-dam Lake Eleanor. The outlet works of the post-dam Lake Eleanor is also in the epilimnion, such that post-dam water temperatures are likely very similar to those under pre-dam conditions. Under natural conditions, summer water temperatures below Lake Eleanor were likely at the upper end of rainbow trout tolerances (Moyle and Baltz 1981); under present conditions, water temperatures at the Eleanor Creek near Hetch Hetchy gaging station (USGS 11-278000) can exceed 70° F (Appendix I). Perhaps the primary difference in water temperature between the pre-dam and post-dam period would be caused by reductions in the snowmelt hydrograph magnitude and duration, which may decrease the length of stream with preferable water temperatures in the spring and early summer.

6.1.3 Riparian Vegetat ion

Information about riparian vegetation specifically related to Eleanor Creek below the dam is limited to the Yosemite National Park Vegetation Inventory; however the inventory was very broad and no local descriptions were included (TNC 1998). The relationship of riparian vegetation dynamics along Eleanor Creek below the dam to substrate, topography and hydrologic environments is described based on qualitative observations made during the 2006 field reconnaissance.

Technical Memo 2 (McBain & Trush and R M C Water and Environment 2006) emphasized that the greatest hydrologic impacts to Eleanor Creek have been in reducing flood peak magnitudes of the less than five-year recurrence flood. Due to the small storage capacity of Lake Eleanor, flood peaks still pass over the dam (i.e., those greater than 5-yr recurrence), scouring the channel and inhibiting riparian woody plant encroachment of the degree seen on Cherry Creek below Cherry Valley Dam. Based on our observations of other regulated and unregulated Sierra Nevada streams, impacts of Eleanor Dam operations on riparian vegetation were not obvious. No riparian encroachment was observed, evidence of frequent riparian woody plant scour was observed, and species diversity and location were comparable to unregulated Sierra Nevada streams. Riparian vegetation growing within the active channel was limited to widely spaced, small individual dusky willow (Salix melanopsis) shrubs, young white alders (Alnus rhombifolia), grasses, and sedges, reflecting an environment that experiences periodic high magnitude flood peaks. Mature white alders were inhibited from growing in the active channel. Adjacent to the active channel in the riparian upland transition, canyon live oak (Quercus chrysolepis) and conifers were

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generally restricted to where the valley toe met the river channel, above the extent of true riparian corridor conditions (Figure 6-7). Canyon live oak and conifers are presumably prevented from encroaching onto active surfaces by the occurrence of frequent and prolonged flood peaks.

Willow species richness is typically low on streams where the snowmelt hydrograph has been reduced or eliminated. Wil low species richness along Eleanor Creek was relatively high compared to streams where the snowmelt hydrograph has been eliminated or reduced. Red willow (Salix laevigata) and arroyo willow (5. lasiolepis) were common, dusky willow was occasionally observed and narrowleaf willow (S. exigua) and shiny willow (S. lucida ssp. lasiandra) were rarely observed. The richness in willow species and the bank locations where they grow suggests that the snowmelt hydrograph was a stronger influence on vegetation pattern than the rainfall hydrograph. Arroyo willow commonality may indicate a subtle shift to increasing influence of the rainfall hydrograph compared to historical (i.e., pre-dam) conditions. Arroyo willow is the earliest seed disperser of the willows observed, and typically disperses its seeds in March and Apr i l (early at lower elevations) often before the snowmelt hydrograph begins to ascend.

The gradation in channel locations for observed species was consistent with observations along other unregulated rivers nearby (e.g., the Clavey River) and the individual woody plant species life histories. There was a strong gradation in the channel locations where the different woody riparian species grew (Figure 6-7). Riparian herbaceous species typically grew on lower bar surfaces close to the low water channel and mature woody riparian species grew on upper bar surfaces 3-4 ft above the summer water elevation. Arroyo willow was common 3-4 ft above the low water surface. White alder was also common, but large individuals (i.e., > 8 inches diameter at breast height) were restricted to channel margins near the toe of the valley slope or areas of hydraulic shadows in boulder gardens or bedrock outcrops (i.e., safe sites, or locations with a "guardian angel"). Dusky willow was occasionally observed within 1-2 ft of the low-water surface.

Figure 6-7: Riparian Vegetation Gradation in Eleanor Creek below Eleanor Dam. Note White Alder Growing at the Upper Active Channel Edge and Ponderosa Pine and Canyon Live Oak Restricted

6.1.4 A n a l y s i s S p e c i e s

Ra inbow Trout

Documented fish fauna in Eleanor Creek and Lake Eleanor consists of rainbow trout, Sacramento sucker, and green sunfish {Lepomis cyanellus) (Baltz and Moyle 1984). The presence of fish in Lake Eleanor is likely the result of human introductions, since natural barriers downstream of Eleanor Dam would have prevented colonization of the reservoir site (formerly a natural lake) following the Pleistocene glaciations. Rainbow trout were stocked in Lake Eleanor as early as 1877 (Hubbs and Wallis 1948, as cited in Moyle and Baltz 1982).

The most complete study of fish habitat, abundance, and population structure in Eleanor Creek was conducted by Moyle and Baltz in 1981 to assess potential effects of pumping water from Lake Eleanor to Cherry Lake via the Eleanor-Cherry Diversion Tunnel on fish in Eleanor Creek and Lake Eleanor. This study included habitat quantification using the Instream Flow Incremental Methodology ( M M ) ,

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quantitative surveys of fish abundance and size at one site downstream of Eleanor Dam and in Lake Eleanor, and temperature monitoring in Eleanor Creek and Lake Eleanor (Table 6-1). Habitat modeling and fish surveys were limited to the 3/4-mile-long, moderate-gradient reach immediately downstream of Eleanor Dam.

Table 6-1: Fish Habitat and Abundance Surveys Available for Eleanor Creek.

Survey/Stud> f Comments Report

7 transects in a 154-foot reach 0.6 miles Habitat quanti f icat ion 8 downstream of E leanor Dam, cal ibrated for f lows of Moyle and Baltz 1981

6 cfs, 20 cfs, and 24 cfs

Trout abundance M u l t i P l e P a w - d e p l e t o n electrofishing in a 108-ft reach during flows of 5 cfs 3

Water temperature June - Sept. 1981 Moyle and Baltz 1981

Water temperature Summer 2006 - present" U S G S

Footnotes: a. Habitat included rainbow trout and Sacramento sucker. b. See Appendix I for data.

The habitat quantification was used to predict available rainbow trout3 habitat area for adult holding, spawning, and juvenile and young-of-year rearing for flows ranging from 2.5 cfs to 50 cfs and was calibrated for flows of 6 cfs, 20 cfs, and 24 cfs. In reaches examined for the study, spawning habitat was limited to small gravel pockets, and no spawning habitat was present in the habitat quantification reach. The quantification, therefore, could not estimate spawning habitat area. The habitat quantification effort also could not be applied to the remainder of the Eleanor Creek Reach because it was unable to predict hydraulic relationships or habitat availability in the steeper channel reaches. Moreover, the habitat quantification did not include temperature as a parameter. The effects of water temperature on habitat suitability, therefore, were not reflected in the habitat quantification results. From these results, Moyle and Baltz (1981) concluded that: (1) adult habitat area responds dramatically to flow and continues to increase beyond the range of flows measured; (2) juvenile habitat area peaks at 45 cfs; and (3) young-of-year habitat area peaks at 25 cfs to 40 cfs (Figure 6-8).

The habitat quantification results represented only flow depth, flow velocity, and channel substrate; they did not reflect the effects of temperature on fish abundance and health nor relationships between flow and temperature. During late summer, water temperature in Eleanor Creek can exceed the upper threshold for adult trout survival. Between July 15 and August 20, 1981, maximum daily water temperature downstream of Eleanor Dam approached 77°F (Figure 6-9) (Moyle and Baltz 1981). High water temperatures are due to a combination of low flows and epilimnionic releases from Lake Eleanor. Unlike many reservoirs, flow released from Lake Eleanor is from the epilimnion, the layer of water above the thermocline. Moyle and Baltz (1981) observed thermal stratification in the reservoir during late summer. Below the thermocline, which was at a depth of 46 ft to 52 ft, water temperature was 54°F; surface water temperature in the reservoir was 72°F to 75°F. The thermocline began breaking up by October 16, when reservoir surface temperature reached 54°F.

The quantification also included habitat for Sacramento sucker.

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Figure 6-8: Predicted Available Rainbow Trout Habitat Area in Eleanor Creek (Moyle and Baltz 1981).

5,000

60

Discharge (cfs)

Moyle and Baltz (1981) concluded that water temperature "may be the most important limiting factor for trout, especially in late summer." Given these temperatures, they concluded that the "potential exists for a summer k i l l of trout i f warm days are combined with low flows, especially in Eleanor and lower Cherry creeks." In additional to direct mortality from chronic or acute exposure, high water temperatures can stunt fish growth. In Eleanor Creek, rainbow trout growth rate is among the poorest recorded for any Sierra stream (Snider and Linden 1981, as cited in Moyle and Baltz 1981), which Moyle and Baltz deduced is "no doubt due to excessively warm, but not critical, stream temperatures during much of the summer." Moyle and Baltz concluded that a minimum flow of at least 15 cfs during summer months was "crucial" for maintaining a viable trout population in Eleanor Creek. Moyle and Baltz (1981) also recommended more gradual reduction in flows after observing stranded fish after flow was reduced to 5 cfs in early summer.

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Figure 6-9: Daily Minimum and Maximum Water Temperature in Eleanor Creek in Summer 1981 (Moyle and Baltz 1981) and Rainbow Trout Temperature Thresholds (Moyle and Marchetti 1992).

t Adult Lelhal

Juvenile Optimal

Adult Preferred Growth

1

Egg/Incubation Optimal

] Eleanor Creek near Hetch Hetchy

-Daily Maximum Temperature

-Daily Minimum Temperature

Adult Lethal

900

600 —

Trout abundance surveys indicated that adult trout density in Eleanor Creek (in 1981) was similar to densities observed in the Upper and Lower Cherry reaches. Observed density of trout > 2 in SL was 9.3 fish/1,000 f t 2 (Moyle and Baltz 1981). Very few young-of-year trout (< 2 in SL) were captured; density was 1 fish/1,000 ft". During our September 2006 field reconnaissance, numerous adult trout were observed in pools in the gorge reach (i.e., from downstream of Moyle and Baltz's study site to the confluence with Cherry Creek). Anecdotally, adult trout density in Eleanor Creek appeared to be higher than in the Upper Cherry Reach and Hetchy Reach.

Foothil l Ye l low- leqqed Frog

No available studies or surveys for foothill yellow-legged frogs or other amphibians in Eleanor Creek were identified during the course of this project. The presence or absence of this species in the reach, therefore, is not known. The reach is within the elevation range of the species, but potential breeding habitat (open cobble bars) is sparse. If foothill yellow-legged frogs do breed in the Eleanor Reach, eggs and larvae would be vulnerable to rapid changes in flow depth and velocity. Eggs laid and larvae hatched during low flow conditions prior to spring spills could be displaced or destroyed after spill begins. Eggs laid along the channel margins and on submerged bars during spring spills, conversely, would be stranded as flow is quickly reduced to summer minimum flow levels. Tadpoles rearing in side channels or other depressions on bars could also be stranded by rapidly dropping flow levels.

Benth ic Macroinvertebrates

No available studies or surveys for benthic macroinvertebrates in Eleanor Creek were identified during the course of this project. Low flows and high water temperatures may limit spring/summer invertebrate production downstream of Eleanor Dam.

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6.2 Cherry Creek - Upper Cherry Reach

6.2.1 G e o m o r p h o l o g y

Sources of geomorphic information on Upper Cherry Creek are few, but more than the Eleanor Reach, Lower Cherry Reach, and the Holm Reach. The primary geomorphic information sources are USGS topographic maps, USGS digital elevation model (DEM), 1953 (pre-dam) ground photos at the U S G S gaging station below Cherry Valley Dam, geomorphic monitoring conducted at a site 1.5 miles downstream of Cherry Valley Dam in 1993 (IRE 1994) and 2006 (McBain & Trush), and our 2006 field reconnaissance. The 1993 and 2006 data collection, including a large right bank cobble/gravel point bar, emphasized cross section surveys, pebble counts, and tracer rocks. The long-term USGS flow data at the Cherry Creek near Hetch Hetchy gaging station (USGS 11-277000) for the pre-dam period and Cherry Creek below Cherry Valley Dam gaging station (USGS 11-277300) for the post-dam period also help explain changes to Cherry Creek geomorphology as a result of Cherry Valley Dam.

Based on our field reconnaissance and the U S G S 10 meter grid D E M , the general setting of Cherry Creek geomorphology is very similar to that of Eleanor Creek. First, glaciers during the Tioga glaciation likely extended downstream of the Cherry Valley Dam site to the confluence of Eleanor Creek. Glaciation upstream of the Cherry Valley Dam site resulted in extensive exposed granite, shallow soils, and sparse forested land above Cherry Lake. From the dam downstream 2 miles to the nick point, the signature from glaciation on the channel is less than on Eleanor Creek, yet the valley remains broader and less confined than downstream of the nick point. The nick point on Cherry Creek where the rapid incision into the uplifting Sierra Nevada range tapers off is more pronounced than on Eleanor Creek (Figure 6-10). As with Eleanor Creek, the morphology of the valley and the stream is markedly different upstream and downstream of the nick point. The gradient (less than 2%) is much less than lower Cherry Creek (4%-5%), and less than the corresponding portion of Eleanor Creek immediately below the dam (2%-3%). In the low gradient portion of the Upper Cherry Reach, the dominant sediment delivery mechanism to the channel is granite block exfoliation and decomposed granitic sand delivery from wind and surface water flow. The substrate upstream of the nick point is small boulder, cobbles, gravel, and sands within a semi-alluvial channel, separated by short steep reaches of exposed granite bedrock.

As was the case for Eleanor Creek, the channel morphology downstream of the nick point is largely shaped by the stream itself, and less so than by glacial processes. The channel is incised within the uplifting Sierra Nevada bedrock, is much steeper (>4%), and very confined by the valley walls. The dominant sediment delivery mechanism to the creek is landslides and rockfalls of fractured granitic blocks from the valley walls. Fires and timber management are very frequent downstream of Cherry Valley Dam, which likely increases fine sediment contribution to the stream. Extensive riparian encroachment in the reach, combined with more severe flow regulation from Cherry Valley Dam, allows much more fine sediment (granitic sand) to deposit in pools, riparian berms, and channel margins in the low gradient reach and the higher gradient reach. The channel geometry has noticeably changed due to fine sediment deposition; in lower gradient semi-alluvial reaches, gravel and sand have deposited along encroaching riparian and upland vegetation, leading to a more rectangular channel. This process was observed at the Cherry Bar monitoring site in 2006, as illustrated on Cross Section 300 (Figure 6-11).

As described in Section 5, the entire range of flood magnitudes from the 1.5 to 25-year flood recurrence has been substantially reduced by flow regulation from Cherry Valley Lake. Therefore, the frequency of bed mobilization has been greatly reduced compared to pre-dam conditions. Based on our cross section surveys, tracer rock data, riparian surveys, and field reconnaissance, the frequency of high flows has been reduced enough to cause extensive riparian and upland vegetation encroachment into the low flow channel, and change channel morphology. Figure 6-12, Figure 6-13, and Figure 6-14 illustrate how riparian and upland vegetation encroachment has occurred between 1953 and 2006. The riparian initiation process along the low flow channel margin likely required only a short time (a few years) after dam

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Figure 6-25: Mapped Available Productive Benthic Macroinvertebrate Area in the Upper Cherry Reach Upstream of Cherry Creek Gorge (McBain & Trush 2006).

26,000

24,000

22,000

20,000

1B.000

16.000

14,000

12,000

10,000

8,000

6,000

4,000

2,000

0

-Entire Reach (2900 It long)

-Less conlined Cherrry Bar Reach (450 ft long)

-Confined Reach (2450 ft long)

1,000

Flow (cfs)

1,800

6.3 Cherry Creek - Lower Cherry Reach

6.3.1 G e o m o r p h o l o g y

The best quantitative information on the Lower Cherry Reach geomorphology is the post-dam USGS flow data at the Cherry Creek near Hetch Hetchy gaging station (USGS 11-278300). This gage is immediately upstream of the Holm Powerhouse and downstream of the Eleanor Creek confluence, so it represents flow contributions from both the Upper Cherry Reach and the Eleanor Reach. Unfortunately, the gage was installed in 1955, preventing a direct comparison with the pre-dam flow regime (annual hydrographs and peak flow data).

As was the case for the high gradient portion of the Upper Cherry Reach, the Lower Cherry Reach is also downstream of the nick point where the rapid incision of the streams into the uplifting Sierra Nevada range tapers off (Figure 6-10). The pre-dam morphology of the valley and stream was very similar to that in the high gradient portion of Upper Cherry Reach, and won't be restated here. A single pre-dam 1953 photo was found for the Cherry Creek near Hetch Hetchy gaging station, and shows a boulder-bed channel with very little riparian vegetation within the active channel (Figure 6-26).

After completion of Cherry Valley Dam, hydrology in the reach was severely regulated; however, the notable exception is that due to the substantial high flow contribution from Eleanor Creek. Riparian and upland encroachment into the channel is much less pronounced, and the geomorphology of the stream functions closer to regional unregulated streams than the Upper Cherry Reach. The substrate of the reach has large boulders over granite bedrock, with cobble, gravel, and sand lee behind large boulders and bedrock outcrops (Figure 6-27).

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FINAL Figure 6-26: Lower Cherry Creek at the USGS Gaging Station Cherry Creek near Early Intake

(Upstream of Holm Powerhouse) in 1953. Present-Day Photo Comparison at Exact Location is not yet Available.

Figure 6-27: Lower Cherry Creek Reach Looking Downstream from Cherry Lake Road Bridge (5 Miles Downstream of Eleanor Creek Confluence). Note Some Riparian Vegetation Encroachment

into the Active Channel, Boulder Substrate with Gravel/Cobble Pockets, and Steep Channel Gradient.

6.3.2 Riparian Vegetat ion

No available studies or surveys of riparian vegetation specifically related to lower Cherry Creek below the confluence of Eleanor Creek to the Holm Powerhouse were identified during the course of this project. The relationship of riparian vegetation dynamics along lower Cherry Creek to substrate, topography and hydrologic environments is described based on a few qualitative observations made during limited field reconnaissance conducted in fall 2006; species richness and spatial distribution/gradation were not assessed.

April 2007 6-27

Upper Tuolumne River: Description of River Ecosystem Chapter 6 Synthesis of Available Information and Recommended Monitoring Actions

FINAL

The influence of the Cherry Valley Dam on flood peaks and snowmelt hydrographs was less evident downstream of the Eleanor Creek confluence than in the Upper Cherry Reach. Valley confinement and contribution of the streamflow from Eleanor Creek inhibit riparian vegetation encroachment into the active channel typical of the Upper Cherry Reach. Alluvial deposits are few in this reach of valley confinement. Where alluvial deposits occur, frequent scour during floods prevents riparian vegetation establishment. Riparian encroachment was evident at some locations, where small patches of vegetation occurred on alluvial deposits in the active channel (Figure 6-27). Species diversity and location was comparable to regulated Sierra Nevada streams with large storage reservoirs.

6.3.3 A n a l y s i s S p e c i e s

R a i n b o w Trout

Documented fish fauna in the Lower Cherry Reach consists of rainbow trout, Sacramento sucker, and Sacramento pikeminnow (Moyle and Baltz 1981, C D F G 1989). One site in the Lower Cherry Reach was included in the Moyle and Baltz (1981) study. Moyle and Baltz (1981) quantified habitat availability for adult holding, spawning, and young-of-year and juvenile rearing for flows up to 100 cfs (Table 6-4). The habitat quantification predicted that adult trout habitat area increases with flow and peaks at 90 cfs, young-of-year habitat area peaks at 35 cfs, and juvenile habitat area peaks at 45 cfs (Figure 6-28). The habitat quantification underestimated spawning habitat area. Trout spawning substrate was limited to small patches in the Lower Cherry Reach; no patches were within the habitat quantification reach. The quantification effort did not assess habitat area during flows exceeding 100 cfs. It is unlikely that habitat area would increase during higher flows in this confined channel reach.

In the 1981 study, density of trout >2 in S L was highest in Lower Cherry Creek (compared to the Upper Cherry and Eleanor reaches). Density of trout >2 in was 1.1 fish/100 ft 2 . Density of trout <2 in was 0.6 fish/100 ft 2, six times higher than the Eleanor Reach but only 25% of young-of-year density observed in the Upper Cherry Reach. C D F G (1989) found that fish standing crop in the Upper Cherry and Lower Cherry reaches were similar, but Upper Cherry stock was entirely rainbow trout while Lower Cherry Creek was dominated by Sacramento suckers. Squawfish were also present at Lower Cherry site. Trout and Sacramento sucker densities during the 1988 C D F G survey were 0.7 fish/100 ft 2 and 1.1 fish/100 ft 2 , respectively ( C D F G 1989). Standing crop of tout and Sacramento sucker were 19.0 lb/ac and 47.5 lb/ac, respectively ( C D F G 1989).

Table 6-4: Fish Habitat and Abundance Surveys Available for Lower Cherry Creek.

Survey/Study Comments Report

Habitat quanti f icat ion 3

6 transects in one 240-foot reach downstream of Cherry Oil R d

bridge, calibrated for f lows of 18 cfs, 24 cfs, and 41 cfs

Moyle and Baltz 1981

1981 snorkel survey within IFIM model r e a c h b

Moyle and Baltz 1981

Trout abundance 1989 multiple pass electrofishing survey 0.75 mi downstream of

Cherry Oil R d C D F G 1989

Water temperature June - Sept. 1981 Moyle and Baltz 1981

Water temperature S u m m e r 2006 - present 0 U S G S

Footnotes: a. Habitat quantification included rainbow trout and Sacramento sucker. b. The study authors considered the results of this survey to be a "ballpark minimum estimate" of trout

abundance. c. See Appendix H for data.

April 2007 6-28

Upper Tuolumne River: Description of River Ecosystem Chapter 6 Synthesis of Available Information and Recommended Monitoring Actions

FINAL

During the 1981 study, maximum daily water temperature reached 70°F (i.e., the upper critical threshold for rainbow trout) during mid-August (Figure 6-29). High water temperatures could reduce or eliminate habitat area suitable for trout in this reach during summer months when flow is low, air temperatures are warm, and inflow from Eleanor Creek is warm. Moyle and Baltz (1981) concluded that "temperature should be a prime consideration when discharges from Lloyd and Eleanor lakes are mixed to meet discharge requirements." Warmer temperatures, however, benefit Sacramento suckers.

Figure 6-28: Predicted Available Rainbow Trout Habitat Area in the Lower Cherry Reach (Moyle and Baltz 1981).

14,000

12,000 -|

— 10,000

8,000

42. 6,000

re X 4,000

2,000

-Juvenile

Young-of-year

- Spawning

- Adult

—• •

40 60

Discharge (cfs)

80 100 120

April 2007 6-29

Upper Tuolumne River: Description of River Ecosystem Chapter 6 Synthesis of Available Information and Recommended Monitoring Actions

FINAL Figure 6-29: Daily Minimum and Maximum Water Temperature in the Lower Cherry Reach in

Summer 1981 (Moyle and Baltz 1981) and Rainbow Trout Temperature Thresholds (Moyle and Marchetti 1992).

Foothil l Ye l low- legged F rog

No available studies or surveys for foothill yellow-legged frogs or other amphibians in Cherry Creek were identified during the course of this project. The current and historic presence or absence of this species in the reach, therefore, is not known. The reach is within the elevation range of the species, and foothill yellow-legged frogs were identified at similar elevations along the Clavey River in surveys conducted by the USFS in 2001 (USFS, unpublished data). This suggests that foothill-yellow legged frogs might potentially occur in this reach. If this species does breed in the reach, it would be sensitive to rapid flow fluctuations from changing releases from Cherry Valley and Eleanor dams.

Benthic Macroinvertebrates

No available studies or surveys for benthic macroinvertebrates in Cherry Creek were identified during the course of this project. Water temperature data from 1981 (the only temperature data available to date; Moyle and Baltz 1981) suggest that warm spring and summer water temperatures may reduce benthic macroinvertebrate production in this reach relative to unregulated conditions.

6.4 Cherry Creek - Holm Reach

6.4.1 G e o m o r p h o l o g y

The best quantitative information on the Lower Cherry Reach geomorphology is the post-dam USGS flow data at the Cherry Creek below Holm Powerhouse gaging station (USGS 11-278400). This gage is approximately half-way between the Holm Powerhouse and the Tuolumne River confluence, and when contrasted with the Cherry Creek near Hetch Hetchy gaging station, effectively isolates the effect of the Cherry Power Tunnel diversion on flows to the reach. Similar to the Cherry Creek near Hetch Hetchy gage, this gaging station was installed in 1962, and there is not a direct comparison with pre-dam flow data. However, this gaging station is downstream of the Holm Powerhouse and all diversions, so the entire natural flow volume of the watershed passes through this reach, albeit severely regulated by upstream reservoirs and Holm powerhouse operation.

April 2007 6-30

Attachment C

• Consider the time necessary to complete facility development activities.

• Develop a contingency plan for implementing appropriate prestorm or winterization BMPs

before the grading permit expires.

• Determine the design capacity, if applicable, ofthe site for public or administrative use,

considering needs for protecting soil, water quality, and riparian resources.

• Ensure that the capacity ofthe site matches the ability of the site to withstand the use.

• Conform to all applicable Federal, State, and local regulations and permits governing water

supply, sanitation, and underground injection systems (see BMP Fac-3 [Potable Water Supply

Systems] and BMP Fac-4 [Sanitation Systems]).

• Determine instream flow needs to minimize damage to scenic and aesthetic values; native plant,

fish, and wildlife habitat; and to otherwise protect the environment where the operation of thefacility would modify existing streamflow regimes (See BMP WatUses-1 [Water Uses Planning]).

Fac-2. Facility Construction and Stormwater Control

None known.

Avoid, minimize, or mitigate adverse effects to soil, water quality, and riparian resources by con­

trolling erosion and managing stormwater discharge originating from ground disturbance during

construction of developed sites.

During construction and operation of facility sites, land may be cleared of existing vegetation and

ground cover, exposing mineral soil that may be more easily eroded by water, wind, and gravity. Changes in land use and impervious surfaces can temporarily or permanently alter stormwater

runoff that, if left uncontrolled, can affect morphology, stability, and quality of nearby streams and other waterbodies. Erosion and stormwater runoff control measures are implemented to retain

soil in place and to control delivery of suspended sediment and other pollutants to nearby surface water. This practice is initiated during the planning phase and applied during project implementa­

tion and operation.

This BMP contains practices for managing erosion and stormwater discharge that are generally ap­

plicable for any project that involves ground disturbance, including developed recreation, mineral

exploration and production sites, pipelines, water developments, etc., and should be used for all

such projects.

Practices Develop site-specific BMP prescriptions for the following practices, as appropriate or when required, using State BMPs, Forest Service regional guidance, land management plan direction,

BMP monitoring information, and professional judgment.

• Obtain Clean Water Act (CWA) 402 stormwater discharge permit coverage from the

appropriate State agency or the U.S. Environmental Protection Agency (EPA) when more than

1 acre of land will be disturbed through construction activities.

• Obtain CWA 4Q4 permit coverage from the U.S. Army Corps of Engineers when dredge or fill

material will be discharged to waters of the United States.

• Establish designated areas for equipment staging, stockpiling materials, and parking tominimize the area of ground disturbance (see BMP Road-9 [Parking Sites and Staging Areas]

and BMP Road-10 [Equipment Refueling and Servicing]).

Manual or Handbook Reference

Objective

Explanation

Volume 1: National Core BMP Technical Guide 41

Attachment C

Establish and maintain construction area limits to the minimum area necessary for completing

the project and confine disturbance to within this area.

Develop and implement an erosion control and sediment plan that covers all disturbed areas, including borrow, stockpile, fueling, and staging areas used during construction activities.

Calculate the expected runoff generated using a suitable design storm to determine necessary

stormwater drainage capacity.

• Use site conditions and local requirements to determine design storm.

• Include run-on from any contributing areas.

Refer to State or local construction and stormwater BMP manuals, guidebooks, and trade

publications for effective techniques to:

• Apply soil protective cover on disturbed areas where natural revegetation is inadequate to prevent accelerated erosion during construction or before the next growing season.

• Maintain the natural drainage pattern of the area wherever practicable.

• Control, collect, detain, treat, and disperse stormwater runoff from the site.

• Divert surface runoff around bare areas with appropriate energy dissipation and sediment

filters.

• Stabilize steep excavated slopes.

Develop and implement a postconstruction site vegetation plan using suitable species and

establishment techniques to revegetate the site in compliance with local direction and

requirements per Forest Service Manual (FSM) 2070 and FSM 2080 for vegetation ecology and prevention and control of invasive species.

Install sediment and stormwater controls before initiating surface-disturbing activities to the extent practicable.

Do not use snow or frozen soil material in facility construction.

Schedule, to the extent practicable, construction activities to avoid direct soil and water disturbance during periods of the year when heavy precipitation and runoff are likely to occur.

• Limit the amount of exposed or disturbed soil at any one time to the minimum necessary to

complete construction operations.

• Limit operation of equipment when ground conditions could result in excessive rutting,

soil puddling, or runoff of sediments directly into waterbodies.

Install suitable stormwater and erosion control measures to stabilize disturbed areas and

waterways before seasonal shutdown of project operations or when severe or successive storms are expected.

Use low-impact development practices where practicable.

Maintain erosion and stormwater controls as necessary to ensure proper and effective functioning.

• Prepare for unexpected failures of erosion control measures.

• Implement corrective actions without delay when failures are discovered to prevent

pollutant discharge to nearby waterbodies.

Routinely inspect construction sites to verify that erosion and stormwater controls are

implemented and functioning as designed and are appropriately maintained.

Use suitable measures in compliance with local direction to prevent and control invasive species.

Volume 1: National Core BMP Technical Guide

• Consider changes or improvements to existing sanitary systems that may be causing water

qualify impacts, such as poorly located pit toilets or drain fields, at opportune times such as

facility remodeling or change in facility ownership or control.

Fac-5. Solid Waste Management

Manual or Handbook Reference FSM 2130; FSM 7460; and FSH 7409.11, chapter 80.

Objective Avoid, minimize, or mitigate adverse effects to water quality from trash, nutrients, bacteria, and chemicals associated with solid waste management at facilities.

Explanation Uncollected garbage and trash at developed facilities can contaminate water by introducing nutri­ents, bacteria, or chemicals to the water. Trash can be blown about by the wind or carried by runoff

into waterbodies. In addition, uncollected garbage can attract wildlife, which are looking for an easy meal, to the facility.

Practices Develop site-specific BMP prescriptions for the following practices, as appropriate or when

required, using State BMPs, Forest Service regional guidance, land management plan direction, BMP monitoring information, and professional judgment

• Develop a Solid Waste System consistent with direction in FSM 7460 and FSH 7409. II, chapter 80 that defines and describes collection, transportation, storage, and final disposal

methods for solid waste generated at facilities.

• Use suitable public relations and information tools and enforcement measures to encourage the public to use proper solid waste disposal measures.

• Encourage recycling of materials where practicable.

• Encourage the public to "pack it in-pack it out" in areas where practicable.

• Provide receptacles for trash at developed facilities.

• Place trash and recycling receptacles in areas that are convenient to the facility's users.

• Place trash and recycling receptacles in locations away from waterbodies.

• Provide receptacles that discourage wildlife foraging as suitable for the area (e.g., bears, raccoons, birds) and suitably confine materials until collected.

• Collect trash on a routine schedule to prevent the receptacles from overflowing.

• Dispose of collected garbage at properly designed and operated municipal-, county-, or State-

authorized sanitary landfills or waste recycling sites where groundwater and surface water are adequately protected.

• Obtain necessary State or local permits for solid waste disposal sites.

Fac-6. Hazardous Materials

Manual or Handbook

Reference 40 CFR U2; FSM 2160; and FSH 2109.14, chapter 60.

Objective Avoid or minimize short- and long-term adverse effects to soil and water resources by preventing releases of hazardous materials.

Volume 1: National Core BMP Technical Guide 45

Explanation Constructing and operating facilities often involve the storage and use of hazardous materials. Im­

proper storage and use can contaminate nearby soils and surface water or groundwater resources.

Practices Develop site-specific BMP prescriptions for the following practices, as appropriate or when

required, using State BMPs, Forest Service regional guidance, land management plan direction, BMP monitoring information, and professional judgment.

• Ensure that all employees involved in the use, storage, transportation, and disposal of hazardous

materials receive proper training.

• Limit the acquisition, storage, and use of hazardous, toxic, and extremely hazardous substances to only those necessary and consistent with mission requirements.

• Manage the use, storage, discharge, or disposal of pollutants and hazardous or toxic substances

generated by the facility in compliance with applicable regulations and requirements.

• Monitor underground storage tanks and promptly address leaking tanks in consultation with the proper officials at State and Federal regulatory agencies.

• Construct and install new tanks in accordance with Federal, State, and local regulations.

• Ensure that existing tanks meet performance standards for new tanks, meet upgrade requirements, or are taken out of service.

• Prepare a certified Spill Prevention Control and Countermeasure (SPCC) Plan for each facility as required by 40 CFR 112.

• Install or construct the containment features or countermeasures called for in the SPCC

Plan to ensure that spilled hazardous materials are contained and do not reach groundwater or surface water.

• Ensure that cleanup of spills and leaking tanks is completed in compliance with Federal,

State, and local regulations and requirements.

• Respond to hazardous materials releases or spills using the established site-specific contingency

plan for incidental releases and the Emergency Response Plan for larger releases.

• Train employees to understand these plans; the materials involved; and their responsibilities for safety, notification, containment, and removal.

• Provide adequate communication to all downstream water users, such as municipal

drinking water providers and fish hatcheries, as necessary.

• Ensure that hazardous spill kits are adequately stocked with necessary supplies and are maintained in accessible locations.

Fac-7. Vehicle and Equipment Wash Water

Manual or Handbook Reference None known.

Objective Avoid or minimize contamination of surface water and groundwater by vehicle or equipment

wash water that may contain oil, grease, phosphates, soaps, road salts, other chemicals, suspended solids, and invasive species.

Explanation Washing vehicles and equipment is a common method used to maintain vehicles and minimize

the spread of noxious and invasive species. Wash water and the resulting residue removed from

vehicles and equipment may contain oils, chemicals, or sediment harmful to water and aquatic re­

sources if not properly contained and treated. Work centers, ranger stations, fire stations, and other

Volume 1: National Core BMP Technical Guida

facilities may have washing equipment and locations designated for cleaning fleet or contracted

vehicles and equipment. Temporary wash locations may also be installed during incident manage­

ment or project work.

Practices Develop site-specific BMP prescriptions for the following practices, as appropriate or when

required, using State BMPs, Forest Service regiona! guidance, land management plan direction,

BMP monitoring information, and professional judgment.

• Use commercial washing facilities that have proper wastewater treatment systems whenever

possible.

• Maintain a list of appropriate wash stations tn the local area and provide the list to local offices, permit holders, and contractors.

• Install temporary wash sites only in areas where the water and residue can be adequately

collected and either filtered on site or conveyed to an appropriate wastewater treatment facility.

• Consider the use of a portable vehicle washer system, such as that designed by the

Missoula Technology and Development System, to contain and filter the wash water.

a Locate temporary wash sites out of AMZs, wetlands, groundwater recharge areas, floodplains, and other environmentally sensitive areas.

• Use suitable measures to treat and infiltrate wash water to comply with applicable surface water and groundwater protection regulations.

Fac-8. Nonrecreation Special Use Authorizations

Manual or Handbook Reference FSM 2720 and FSH 2709.11, chapters 40 and 50.

Objective Avoid, minimize, or mitigate adverse effects to soil, water quality, and riparian resources from physical, chemical, and biological pollutants resulting from activities under nonrecreation special

use authorizations.

Explanation This BMP covers all nonrecreation special use activities with the exceptions of pipelines; transmis­

sion facilities and other rights-of-ways; and water diversions, storage, and conveyance. BMP Fac-9 (Pipelines, Transmission Facilities, and Rights-of-Way), BMP WatUses-4 (Water Diversions and

Conveyances), and BMP WatUses-5 (Dams and Impoundments) are provided for those activities.

The Forest Service role in defining and requiring the use of BMPs occurs during the development of the special use authorization and administration of the use. Discussions between the Forest

Service and the permit holder concerning soil, water quality, and riparian resource impacts and ap­propriate BMPs to use should occur at the time of permit development or renewal. The special use

authorization operation and maintenance plan details the conditions that must be met, including

management requirements and mitigation measures to protect water quality. The permit holder will be required to conform to all applicable Federal, State, and local regulations and land management

plan direction governing water resource protection and sanitation. State or Federal law may require

that the permit holder obtain a pollution discharge pennit or other authorization from a State, re­

gional, or local government entity. Authorized uses often cover a wide range of activities and may

require that BMPs from several management activity categories be included in the authorization.

Practices Develop site-specific BMP prescriptions for the following practices, as appropriate or when

required, using State BMPs, Forest Service regional guidance, land management plan direction,

BMP monitoring information, and professional judgment.

Volume 1: National Core BMP Technical Guide 47

Attachment D

WEPP Soil Erosion Analysis for LCAER Project

The USFS WEPP (Water Erosion Prediction Project) tool was use to estimate erosion for three locations on the LCAER project, Kelly point staging area, canal reach 3 road & aerial pipe section road. The analysis duration was 1 year. The following inputs were used to run the model on each respective location.

Kelly point Reach #3 Aerial Pipe

Climate: Hetch Hetchy Hetch Hetchy Hetch Hetchy Soil Texture: Sandy Loam Sandy Loam Sandy Loam Rd. Design: Out Sloped Un rut Out Sloped Un rut Out Sloped Un rut Road Gradient: 1% 1% 1% Length: 150’ 1000’ 434’ Width: 143’ 12’ 12’ Fill Gradient: 40% 50% 50% Length: 25’ 40’ 45’ Buffer Gradient: 75% 65% 70% Length: 970’ 1000’ 877’ Results Rd prism erosion: 2,806 lb/yr. 5,317 lb/yr. 90 lb/yr.

Provisional values for $trafficx traffic

Run description:

WEPP files: [ slope | soil | vegetation | weather | response || results ]

WEPP:Road Results

INPUTS

Climate HETCH HETCHY CA

Soil texture sandy loam with 20% rock fragments (road: 20%; fill: 20%; buffer: 20% rock)

Road design Insloped, vegetated or rocked ditch

Surface, traffic native surface, no traffic

Gradient (%)

Length (ft)

Width (ft)

Road 1 434 12

Fill 50 45

Buffer 70 877

1 - YEAR MEAN ANNUAL AVERAGES

Total in 1 years

33.74 in precipitation from 67 storms

0.04 in runoff from rainfall from 8 events

0.36 in runoff from snowmelt or winter rainstorm from 7 events

21.35 lb road prism erosion

2201.31 lb sediment leaving buffer

Aerial Pipe Road section Add to log

Return to Input Screen

WEPP:Road results version 2012.12.31 based on WEPP VERSION 2010.100 by Hall and Anderson; Project leader Bill Elliot USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843 05:00 pm Thursday October 9, 2014 GMT 10:00 am Thursday October 9, 2014 Pacific Time WEPP:Road run ID wepp-12659

Page 1 of 1WEPP:Road Results

10/9/2014http://forest.moscowfsl.wsu.edu/cgi-bin/fswepp/wr/wr.pl

Provisional values for $trafficx traffic

Run description:

WEPP files: [ slope | soil | vegetation | weather | response || results ]

WEPP:Road Results

INPUTS

Climate HETCH HETCHY CA

Soil texture sandy loam with 20% rock fragments (road: 20%; fill: 20%; buffer: 20% rock)

Road design Outsloped, unrutted

Surface, traffic native surface, low traffic

Gradient (%)

Length (ft)

Width (ft)

Road 1 1000 12

Fill 50 40

Buffer 65 1000

1 - YEAR MEAN ANNUAL AVERAGES

Total in 1 years

33.74 in precipitation from 67 storms

0.00 in runoff from rainfall from 5 events

0.00 in runoff from snowmelt or winter rainstorm from 7 events

5317.50 lb road prism erosion

721.00 lb sediment leaving buffer

WEPP Run Reach 3 Road Add to log

Return to Input Screen

WEPP:Road results version 2012.12.31 based on WEPP VERSION 2010.100 by Hall and Anderson; Project leader Bill Elliot USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843 03:33 pm Thursday October 9, 2014 GMT 08:33 am Thursday October 9, 2014 Pacific Time WEPP:Road run ID wepp-7668

Page 1 of 1WEPP:Road Results

10/9/2014http://forest.moscowfsl.wsu.edu/cgi-bin/fswepp/wr/wr.pl

Provisional values for $trafficx traffic

Run description:

WEPP files: [ slope | soil | vegetation | weather | response || results ]

WEPP:Road Results

INPUTS

Climate HETCH HETCHY CA

Soil texture sandy loam with 20% rock fragments (road: 20%; fill: 20%; buffer: 20% rock)

Road design Outsloped, unrutted

Surface, traffic native surface, low traffic

Gradient (%)

Length (ft)

Width (ft)

Road 1 150 143

Fill 40 25

Buffer 75 970

1 - YEAR MEAN ANNUAL AVERAGES

Total in 1 years

33.74 in precipitation from 67 storms

0.01 in runoff from rainfall from 5 events

0.05 in runoff from snowmelt or winter rainstorm from 7 events

2806.21 lb road prism erosion

730.36 lb sediment leaving buffer

Kelly Pt. Add to log

Return to Input Screen

WEPP:Road results version 2012.12.31 based on WEPP VERSION 2010.100 by Hall and Anderson; Project leader Bill Elliot USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843 03:38 pm Thursday October 9, 2014 GMT 08:38 am Thursday October 9, 2014 Pacific Time WEPP:Road run ID wepp-8048

Page 1 of 1WEPP:Road Results

10/9/2014http://forest.moscowfsl.wsu.edu/cgi-bin/fswepp/wr/wr.pl