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U.S. GEOLOGICAL SURVEY
Scientific Investigations Report 2007–5173

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Introduction

In March 2003, 16,500 acres of salt evaporation ponds owned by the Cargill Corporation in the San Francisco Bay estuary were purchased using State, Federal, and private funds. Currently, the California Coastal Conservancy is leading a collaborative planning effort with the U.S. Fish and Wildlife Service (USFWS) and the California Department of Fish and Game (DFG) to restore some of the ponds to tidal action while providing for flood management, public access, and recreation.

The draft restoration plan envisions restoration of 50 to 90 percent of the acquired ponds within 50 years (South Bay Salt Pond Restoration Project, 2007). The ponds will be operated and maintained according to the South Bay Salt Ponds Initial Stewardship Plan (ISP) until they are restored. The goals of the ISP are to maintain existing wildlife habitat and to prevent a build up of salt in the ponds in a cost-effective manner until the long-term restoration plan is in effect (Life Science! Inc., 2003).

A salt-pond box model (SPOOM) was developed by Lionberger and others (2004) to simulate water volume and salinity of a salt pond for use in estimating water and salinity budgets for ponds in the Napa–Sonoma Salt Pond Complex. The model uses the principle of conservation of mass to calculate daily pond volume and salinity and includes a salt crystallization and dissolution algorithm. Model inputs include precipitation, evaporation, infiltration, and water transfers. SPOOM was reconfigured to simulate volume and salinity for a portion of the purchased South Bay salt ponds, Alviso salt ponds A9–A17 (fig. 1), and a temperature subroutine was added. SPOOM will be used by the USFWS to assist with the management of the ponds as bird habitat.

Purpose and Scope

This report documents the changes made to SPOOM to simulate salt-pond function for Alviso salt ponds A9–A17 in South San Francisco Bay. Changes to the model include input data and boundary conditions specific to the Alviso salt pond area, the ability to simulate conditions for the entire system of ponds in one simulation run rather than just for an individual pond, and a new temperature subroutine to simulate daily average, minimum, and maximum pond temperature. The temperature subroutine was validated by comparing simulated pond temperatures to hourly and monthly temperature data collected in pond 3 of the Napa–Sonoma Salt Pond Complex and Alviso salt pond A14. This report also describes how the model can be used by the USFWS to achieve pond salinity and depth goals of the ISP. The user is able to specify the connectivity between ponds, how screw gates and combination gates are controlled, and the vertical datum and unit systems used during the simulation.

This modification of the original SPOOM represents the specific conditions of the Alviso salt ponds only and cannot directly be used to simulate salt-pond function elsewhere. Nevertheless, this report illustrates how similar modifications can be made to the basic SPOOM model (Lionberger and others, 2004) to simulate pond geometries, hydraulic structures, tidal effects, and meteorological input data applicable to other salt ponds in other locales.

Description of the Study Area

Commercial salt production in South San Francisco Bay began in the 1850s during the gold rush when dikes were built around salt marshes for the collection and evaporation of seawater. By the 1930s, almost half of the South Bay’s historical tidal marshes had been converted into salt ponds (San Francisco Estuary Institute, 1999). In 1974, approximately 13,000 acres of South Bay salt ponds were sold to the Federal Government by the Leslie Salt Company to form the San Francisco Bay National Wildlife Refuge, now managed by the USFWS. The Alviso ponds were included in this transaction. The Leslie Salt Company retained the mineral rights to the ponds and continued to use the ponds for salt production until it sold all its existing land holdings and mineral rights to the Cargill Corporation in 1978. In March 2003, Cargill sold 16,500 acres of salt ponds and mineral rights to DFG and USFWS.

Historically, salt was produced during the spring through the fall dry season by evaporation of water from the ponds. Water entered the pond system from intakes in the southwestern ponds and flowed by gravity sequentially through the pond system toward the Newark Plant site where the evaporation process was completed and the salt harvested.

The bathymetry of Alviso ponds A9–A17 was surveyed by the USGS in summer 2002, fall 2003, and spring 2004. Pond depths were measured using a single beam echo sounder or an acoustic Doppler current profiler (Takekawa and others, 2003), and pond bottom elevations were determined in reference to USGS benchmark elevations. Concurrent measurements of location in the ponds were made using the global positioning system, and contour maps were prepared to enable the calculation of pond volumes for any depth of water. Table 1 summarizes the survey results for a pond water-surface elevation of 1.5 feet, NGVD 29.

The seven-pond system has been modified from its original flow pattern as specified by the ISP. The system consists of a set of flow-through ponds A9 (intake), A10, A11, and A14 (outlet), batch ponds A12, A13, and A15 (intake), and two other flow-through ponds, A16 (intake) and A17 (outlet). Slough water flows through the ponds by gravity through culverts equipped with flap gates and screw gates to control water movement. Outlet ponds are also equipped with removable weirs to control minimum pond depths when needed. The batch ponds are operated as high-salinity ponds, through which water is moved, as needed, to maintain target salinities and water depths. Intake and outlet pond culverts are equipped with combination gates that function as either a screw gate or as a flap gate allowing for unidirectional, bidirectional, or no flow. A pump is located in pond A13 to pump either to pond A14 or A15 at a rate of 22,000 gallons per minute (gal/min). A pump also is located in pond A8 to transfer water into pond A11 at a rate of 4,000 gal/min.

The Alviso salt ponds are located within the Pacific Flyway and serve as staging and wintering areas for migratory waterfowl and shorebirds (Harvey and others, 1992). Water level, salinity, and temperature are key habitat criteria for bird use and food supply (Takekawa and others, 2001; 2006). Accordingly, target water levels and salinities for each pond have been specified by the ISP (table 2).

Winter inflow controls also have been specified by the ISP to minimize entrainment of salmonids. Thus, ponds A9 and A15 are closed to tidal inflow and the intake-outlet circulation of pond A16 and A17 are reversed from December 1 to May 31. Pond A14 is closed to tidal flow from December 1 to April 30, although bidirectional tidal flow is allowed during May to maintain salinity levels below 40.

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