This annual report summarizes the results of the 2009 water quality sampling conducted at the Alviso Ponds in Santa Clara County, California, which are part of the South San Francisco Bay (Bay) Low Salinity Salt Ponds. Operations occurred from June through October 2009. Sampling was performed on a continuous, weekly, monthly, or bi-monthly schedule as required by the California Regional Water Quality Control Board (RWQCB) Final Order (No. R2-2004-0018). Sampling was performed by the United States Geological Survey (USGS) on behalf of the United States Fish and Wildlife Service (FWS) in accordance with the waste discharge requirements.

The Final Order for the South San Francisco Bay Low Salinity Salt Ponds concerned 15,100 acres of ponds in Alameda, Santa Clara, and San Mateo Counties. The area encompasses the Alviso Pond Complex (Figure 1-1). This report covers the following pond systems within the complex: A3W, A7, A14, and A16. The systems are operated by the Don Edwards San Francisco Bay National Wildlife Refuge (Refuge) in Santa Clara County. The California Department of Fish and Game (CDFG) will submit a report for the Eden Landing (Baumberg) Ponds under a separate cover.

The ponds are generally being operated as flow-through systems with Bay or slough water entering an intake pond within each pond system at high tides through a tide gate, passing through one or more ponds, and exiting the particular system]s discharge pond to either a tidal slough or the Bay at low tides. The ponds only discharge at low tides for about 6 or 8 hours per day. Two ponds in the A3W and A7 systems, Ponds A3N and A8, respectively, were operated as seasonal ponds during 2009 and were not connected to this flow-through system. Also, Ponds A12, A13, and A15, part of the A14 pond system, are designed as batch ponds. Discharge occurs from Pond A15 to Pond A16 when salinity reaches over 130 parts per thousand (ppt); it was not discharged on a batch basis in 2009.

The Final Order recognized two periods of discharges from the ponds. The first covered the Initial Release Period (IRP) when salinity levels would decrease from the initial levels in the ponds. The second period is the Continuous Circulation Monitoring (CCM) period after salinities went below the 44 ppt salinity discharge limit. Different monitoring plans were identified in the Final Order by RWQCB and revised in 2005 (March 25, 2005 letter) and 2008 (June letter) for each specific period and are reiterated below.