AGENCY: Fish and Wildlife Service, Interior (Lead Agency NEPA) California Department of Fish and Game (Lead Agency CEQA).

ACTION: Notice of Intent to Prepare a Joint Environmental Impact Statement/Environmental Impact Report for the South Bay Initial Stewardship Project. 

SUMMARY:  The U.S. Fish and Wildlife Service (USFWS) and the California Department of Fish and Game (CDFG) are preparing a joint Environmental Impact Statement/ Environmental Impact Report (EIS/EIR) to address the potential impacts of the Initial Stewardship Project for the South Bay Salt Ponds (ISP) in south San Francisco Bay, California. The joint EIS/EIR will address the design, implementation, and maintenance of the proposed ISP to comply with the National Environmental Policy Act (NEPA) and the California Environmental Quality Act (CEQA), and all necessary permits and approvals from other local, state, and federal agencies.

This notice describes the proposed action and possible alternatives; notifies that an EIS/EIR will be prepared and considered; invites the participation of other Federal, State and local agencies, affected Tribes, and the public in the process for determining the scope of issues to be addressed and for identifying the significant issues related to the proposed action (the scoping process); and describes the proposed scoping process, including the scoping meeting to be held.

DATES: A public scoping meeting to solicit comment on the environmental effects of the ISP and the scope and significant issues to be analyzed in the EIS/EIR will be held on March 27, 2003 from 7:00 pm to 9:00 pm at the Visitor Center, Don Edwards San Francisco Bay NWR, #1 Marshlands Road, Fremont, California.  Call (510) 792-0222 if directions are needed.  Persons needing reasonable accommodations in order to attend and participate in the public scoping meeting should contact the Refuge Manager at (510) 792-0222 sufficiently in advance of the meeting to allow time to process the request.   Written comments are encouraged and should be received on or before April 20, 2003.

ADDRESSES:  Information or comments related to the NEPA process should be submitted to Refuge Manager, San Francisco Bay NWR Complex, P.O. Box 524, Newark, CA 94560.  Written comments may also be sent by facsimile to (510) 792-5828. All comments received, including names and addresses will become part of the administrative record and may be made available to the public.


Questions regarding the NEPA process, including scoping may be directed to  Margaret Kolar, Refuge Manager, U.S. Fish and Wildlife Service, San Francisco Bay NWR Complex, P.O. Box 524, Newark, California 94560 (telephone (510) 792-0222). For questions concerning the CEQA process, please contact Carl Wilcox, Habitat Conservation Manager, California Department of Fish and Game, Region 3 Headquarters, P.O. Box 47, Yountville, CA  94599 (telephone (707) 944-5525).


Project Location

The USFWS and CDFG will acquire from Cargill Salt, 15,100 acres of industrial solar salt ponds and/or associated salt-making rights in south San Francisco Bay, California. Under terms of the acquisition, the USFWS will own and manage 8,000 acres of "Alviso Ponds," the 1,600 acres of "West Bay Ponds." The CDFG own and will manage 5,500 acres of ìBaumberg Ponds.î   

The Alviso Ponds consist of an 8,000-acre complex of 25 ponds on the shores of the South Bay in Fremont, San Jose, Sunnyvale and Mountain View, in Santa Clara and Alameda Counties. Palo Alto Baylands Nature Preserve and Charleston Slough border the acquisition area on the west, on the south by Moffet Naval Air Station, Sunnyvale Baylands Park and to the east by Coyote Creek and Cushing Parkway in Fremont. Major drainages which discharge into San Francisco Bay within the complex area include Charleston Slough, Mountain View Slough, Stevens Creek, Guadalupe Slough, Alviso Slough (Guadalupe River), Artesian Slough, Mud Slough, and Coyote Creek. The complex includes three ìIsland Pondsî surrounded by Coyote Creek and Mud Slough.

The West Bay Ponds consist of a 1,600-acre complex of 7 ponds on the bay side of the Peninsula, on both sides of Highway 84 west of the Dumbarton Bridge, bayward of the developed areas of the City of Menlo Park in San Mateo County. Bayfront Park is located to the west, and the Dumbarton Bridge approach and the UPRR are located at its southern border. Ravenswood Slough discharges to the Bay through the complex.

The Baumberg Ponds consist of a 5,500-acre complex of 23 ponds on the shores East Bay, west of Hayward and Union City in Alameda County. The approach to the San Mateo Bridge and the CDFG Eden Landing Ecological Reserve, form the northern boundary of the acquisition area. Alameda Creek Flood Control Channel and the Coyote Hills form the southern boundary. Major drainages that discharge into the San Francisco Bay within the complex include Old Alameda Creek and Alameda Creek Flood Control Channel.

Project Description

The proposed South Bay Salt Ponds Initial Stewardship Project is intended to provide for management of the ponds from the time management responsibility is transferred by Cargill to the USFWS and CDFG until a long-term restoration and management plan for the South Bay is completed. It is anticipated that the planning and design process for long-term restoration, and thus the duration of the ISP, will require at least five years.

The objectives of the proposed South Bay Salt Ponds Initial Stewardship Project include:

1.  Cease salt production;

2.  Circulate bay water through the ponds and introduce tidal hydrology to ponds where feasible;

3.  Maintain existing open water and wetland habitat for the benefit of wildlife, including habitat for migratory shorebirds and waterfowl and resident breeding species;

4.  Maintain ponds in a restorable condition to facilitate future long term restoration;

5.  Meet all regulatory requirements, including discharge requirements to maintain water quality standards in the South Bay.

Proposed changes to existing operations include:

1.  Circulating bay waters through reconfigured pond systems and releasing pond contents into the Bay. The plan will require installing new water control features, consisting of intake structures, outlet structures and additional pumps to maintain existing shallow open water habitat.

 2.  Managing a limited number of ponds as seasonal wetlands, to reduce management costs and optimize habitat for migratory shorebirds and waterfowl.

3.  Managing different summer and winter water levels in a limited number of ponds to reduce management costs and optimize habitat for migratory shorebirds and waterfowl.

4.  Restoration of three ponds to muted tidal or full tidal influence.

5.  Managing several ponds in the Alviso system as ìbatch pondsî, where salinity levels would be allowed to rise in order to support specific wildlife populations.

Installation of all proposed water control structures is anticipated to require several years to complete. After water control structures are installed for individual pond systems, intake of bay water into ponds and initial release of pond contents into the Bay will generally begin the following March to May time period when salinities within ponds and in the Bay are at their lowest. During the initial release period, the discharge salinity from the pond system may be significantly higher than normal Bay salinity. Three levels of maximum initial release salinity conditions are proposed in Table 1. Ponds were designated for a particular salinity group based on the historic operation of the salt operations and system constraints on changes to the existing salinities. Salinity group 1 ponds would have a maximum initial discharge salinity of 65 parts per thousand (ppt). (Seawater is approximately 32 ppt.)  These ponds are generally intake ponds or ponds near intakes with the lowest existing and historic salinities. Salinity group 2 ponds would have a maximum initial discharge salinity of 100 ppt. These ponds are in the middle range of the ponds in the acquisition. Salinity group 3 ponds would have a maximum initial discharge salinity of 135 ppt.

For Alviso systems expected water depths in most of the ponds will be 1 to 2 feet on average, similar to their existing condition. Average water depths in the Baumberg systems will range from zero to about 2.5 feet in summer, and about 1 to 2.5 feet in winter.  To save on pumping costs, water surface levels in the Baumberg systems will be operated at levels lower than existing conditions. Eliminating pumping in winter will result in different operating water levels between summer and winter. The West Bay Ponds will be managed in a similar manner to current salt making operations for at least three years. During this period, high salinity brines will be moved to the Cargill Newark Plant Site. Intake structures needed for the ISP may also be used during this period. Management plans and hydrologic modeling for Initial Stewardship will be completed during that time.

Preliminary Alternatives Identified to Date

The EIS/EIR will consider a range of actions, alternatives and impacts, including the no action alternative.  Scoping is an early and open process designed to determine the issues and alternatives to be addressed in the EIS/EIR.  To date, the following alternatives have been identified.

No Action

Under the No Action alternative, there would be no flow circulation through the pond systems. No additional water control structures would be installed, no release of pond contents or management of water and salinity levels would occur, and the existing infrastructure would not be maintained. The contents of the ponds would be allowed to evaporate leaving behind salt-crusted flats and in deeper areas, residual pools of concentrated brine. Ponds would take 1 to 2 years to dry. The deepest portions of the ponds will be seasonally wet during winter, filling with water after rain events. Under the No Action alternative, most of the existing open water habitats currently used by wildlife would be eliminated. Without maintenance pond levees and control structures would be prone to failure, increasing risk of uncontrolled intake and release of flows from/to the Bay. Although this alternative minimizes additional inputs of salinity, long-term pond drying may result in hyper-saline soil conditions. This may cause the chemistry of the soil to be affected in a manner that would likely increase the cost and level of effort of future restoration.

Maintain Infrastructure Only

This alternative is the same as the No Action alternative except that the levees and water control structures would be maintained and repaired as needed. The ponds would be managed as seasonal ponds until the final restoration plan has been completed. Under this scenario the pond contents would be removed or allowed to evaporate. During the summer, they would be maintained as dry to minimize construction and management costs. During winter they would fill during precipitation events but contents would not be discharged. Maintenance of the levees and water control structures would prevent their deterioration that could cause the accidental breaching of the ponds and release of pond contents to the Bay. Under this alternative, most of the existing open water habitats currently used by wildlife would be eliminated, significantly changing the character of the South Bay salt ponds. This alternative minimizes additional inputs of salinity and does not require a permit to discharge pond contents into the Bay.  As with the No Action alternative, long-term pond drying may result in hyper-saline soil conditions. This may cause the chemistry of the soil to be affected in a manner that would likely increase the cost and level of effort of future restoration.

Breach Levees of Island Ponds A19, A20 and A21

Under the proposed action, the Island Ponds would be retrofitted with new intake and outlet structures, and managed under a muted tidal condition. Breaching of the levees of each pond would allow the three ponds to return to a more natural tidal regime. Due to their location between Lower Coyote Creek and Mud Slough, the Island Ponds are fairly inaccessible, and therefore, difficult to actively manage. They would be inundated during the high tides but would be above water at other times resulting in 474 acres of intertidal marsh and mudflat habitat. Concerns regarding the breach alternative include increasing the tidal prism of Coyote Creek as well as altering the existing deposition and scour regime of Coyote Creek. Specifically, there is a concern that increased velocities in Coyote Creek could cause scour at the railroad crossing of Coyote Creek.

Seasonal Pond Operations

Under the proposed action, pond systems consisting of numerous ponds generally have one or more pond(s) serving as batch ponds. Due to their location and, in some cases, relatively high bottom elevations, batch ponds do not have continuous water circulation. They do not have a direct hydrologic connection to the bay or tidal sloughs and creeks, but rely on a neighboring pond for delivery of inflows and release of outflows. The volume and frequency of the intake and release from/to a neighboring pond are used to control the batch pond salinity and water levels. Batch ponds can easily be managed for high salinity in the range of 80-120 ppt to favor brine shrimp and brine fly production, an important food source to certain waterfowl.

As an alternative to a batch pond, certain ponds could be operated as a seasonal pond to eliminate costly pumping during summer to maintain water levels. Seasonal ponds differ from batch ponds in that their contents would be drained prior to summer. Seasonal ponds will fill from rain during winter and be allowed to dry-down through the summer. The pond salinity would not be controlled, but would fluctuate due to residual salt in the pond, rainwater inflows, and seasonal evaporation.

Flexibility in Time Period of Initial Release

Under the proposed action, initial discharge of pond contents would begin in March/April when salinities within the ponds and receiving waters are the lowest. Allowing initial release of pond contents into the Bay at other times during the year would be desirable as a contingency since all necessary water control structures cannot be installed prior to the initial March/April release date. In addition, for certain Alviso ponds, discharge at other time periods would avoid entrainment of juvenile salmonids during downstream migration periods. Concerns regarding this alternative include the ability to meet regulatory requirements for the initial discharge of pond contents and effects of elevated salinity at discharge locations to upstream migrating adult salmonids and bay shrimp.

Table 1  Salinity Groups

Salinity Group

Maximum Initial Discharge  Salinity

Alviso Complex Ponds

Baumberg Complex Ponds

West Bay Complex Ponds

Group 1

65 ppt

A1, A2W, A2E, B1, B2, A3W, A3N

1, 2, 4, 7

10, 11


Group 2

100 ppt

A5*, A7*,A8*

A9, A10, A11, A14

5, 6, 1C, 2C, 3C, 4C, 5C, 6C


Group 3

135 ppt

A12, A13, A15

A16, A17

A19, A20, A21

6A, 6B

9, 8A, 8


1, 2, 3, 4, 5, 5S,



* These ponds would have a maximum initial discharge salinity level of 110 ppt 

Content of the EIS/EIR

The EIS/EIR will analyze, describe, and evaluate direct, indirect and cumulative potential environmental impacts of alternatives, including the no project/no action alternative in accordance with NEPA and CEQA. The range of alternatives being considered may be refined, expanded, or revised as a result of the scoping process. Impact analysis will include a discussion of direct and indirect impacts, short- and long-term impacts, cumulative impacts, and unavoidable impacts. For each issue listed below, the EIS/EIR will include a discussion of the parameters used in evaluating the impacts; recommended mitigation, indicating the effectiveness of mitigation measures proposed to be implemented and what, if any, additional measures would be required to reduce the impacts to below a level of significance. Direct and indirect impacts that will be analyzed include disturbance during construction of water control structures, changes in pond water depth and salinity, changes to water quality in the receiving Bay, creeks and sloughs, and effects caused by operation and maintenance.

The list of issues presented below is preliminary both in scope and number. These issues are presented to facilitate public comment on the scope of the EIS/EIR, and are not intended to be all-inclusive or to be a predetermination of impacts to be considered.

Water Quality

The EIS/EIR will describe existing water quality conditions in the salt ponds within the project area and the receiving waters; characterize effects of discharges including changes in salinity, turbidity, dissolved oxygen, BOD, and metals; and consider potential effect of the timing of discharges as well as the specific location of discharges.


The EIS/EIR will describe existing contaminant levels in sediments of the salt ponds and adjacent Bay, creek and sloughs including chromium, copper, lead, nickel, silver, zinc, arsenic, cadmium and mercury; and consider potential effects of water level management in remobilization of buried contaminants.

Biological Resources

The EIS/EIR will describe existing habitat and characterize changes in wildlife habitat and wildlife use in ponds and receiving waters. The EIS/EIR will also identify potential sensitive species and habitats in or near the project area and determine their abundance and extent of sensitive habitats that may be impacted by project implementation. Specific species to be addressed include California clapper rail, snowy plover, California least tern, salt marsh harvest mouse, Chinook salmon and steelhead trout.

Air Quality

The EIS/EIR will evaluate effects of changes in water quality and water elevations that may cause the release of hydrogen sulfide and other odorous organic gases.

Flood Protection

The EIS/EIR will evaluate effects of introduction of water circulation into ponds to changes in flood protection to neighboring developments.


The EIS/EIR will evaluate effects of the project to commercial fishing of Bay shrimp, including the initial release of pond contents to sloughs and creeks were juveniles are found.

Cumulative Impacts

The EIS/EIR will examine the cumulative impacts of past, ongoing, and probable future projects affecting tidal marsh and estuarine habitats in the South Bay. Projects will include other salt pond restoration projects and wetland habitat improvement project.

Scoping Process

The EIS/EIR will be prepared in compliance with NEPA and Council on Environmental Council Regulations, contained in 40 CFR parts 1500 - 1508; and with CEQA, Public Resources Code Sec 21000 et seq., and the CEQA Guidelines as amended.  Because requirements for NEPA and CEQA are somewhat different, the document must be prepared to comply with whichever requirements are more stringent.  The Service will be the lead agency for the NEPA process and the Department of Fish and Game will be the lead agency for the CEQA process.  In accordance with both CEQA and NEPA, these lead agencies have the responsibility for the scope, content, and legal adequacy of the document.  Therefore, all aspects of the EIS/EIR scope and process will be fully coordinated between these two agencies.

The draft EIS/EIR will incorporate public concerns associated with the project alternatives identified in the scoping process and will be distributed for at least 45-day public review and comment period. During this time, both written and verbal comments will be solicited on the adequacy of the document. The final EIS/EIR will address the comments received on the draft during public review and will be made available to all commenters on the draft EIS/EIR and anyone requesting a copy during the 45-day public review period. The final EIS/EIR shall (1) provide a full and fair discussion of the proposed actionís significant environmental impacts, and (2) inform the decision-makers and the public of reasonable measures and alternatives that would avoid or minimize adverse impacts or enhance the quality of the human environment.

The final step in the Federal EIS process is the preparation of a Record of Decision (ROD), a concise summary of the decision(s) made by the USFWS. The ROD can be published immediately after the final EIS comment period has ended. The final step in the State EIR process is certification of the EIR, which includes preparation of a Mitigation Monitoring and Reporting Plan and adoption of its findings, should the project be approved.  A certified EIR indicates the following: (1) The document complies with CEQA; (2) the decision-making body of the lead agency reviewed and considered the final EIR prior to approving the project; and (3) the final EIR reflects the lead agencyís independent judgment and analysis.

This notice is provided pursuant to regulations for implementing the National Environmental Policy Act of 1969 (40 CFR 1506.6).

March 27, 2003