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Science Support for Wetland Restoration in the
Napa-Sonoma Salt Ponds, San Francisco Bay
Estuary: An Assessment of Fish Use

The Problem

Over the past 150 years, land reclamation activities have resulted in loss of significant amounts of tidal marshes (sometimes referred to as intertidal wetlands, the estuarine zone that is alternately flooded and exposed) in San Francisco Bay and the Sacramento-San Joaquin Delta (Bay/Delta). These marshes and adjacent subtidal waters serve as year-around habitats for forage fishes and as nurseries for larval or juvenile life stages of many other fishes, including those of recreational and commercial importance. Recently, in an effort to halt or reverse the decline of fish and wildlife populations in the Bay/Delta, agricultural fields, salt ponds, and other lands of marginal economic value that historically functioned as tidal marshes were converted back to marsh habitats. The value of these restored tidal marshes to fishes must be assessed to determine if further management actions are needed to enhance the restoration process. An added concern is that residual contamination from past use of agricultural pesticides, fertilizers, petroleum waste products, and other chemicals might adversely affect fish or their food chains. The purpose of this study is to describe the value of restored tidal marshes as habitat for estuarine fishes in the Bay/Delta.

Results from this study will allow resource planners from federal, state, and local agencies such as U.S. Fish and Wildlife Service, U.S. Army Corps of Engineers, California Department of Fish and Game, and San Francisco Bay Conservation and Development Commission to better design and manage restored tidal marshes in the Bay/Delta so that they closely simulate ecological conditions found in natural tidal marshes.

Objectives

This subtask is designed to (i) compare abundance and composition of estuarine fishes among ponds, document food habits of selected species, and relate to fish-forage organisms and hydrological conditions, and (ii) in conjunction with other studies, present a conceptual model of fish use with respect to hydrology, water quality, primary productivity, invertebrate abundance, and flows and sediments along a salinity gradient.

To better focus the objectives of this subtask, value is equated to ecological importance. Thus, a particular tidal marsh has a higher relative value as habitat for a given fish species if the fish population is higher in density than in another marsh.

Methodology

This subtask is part of a broader multi-agency investigation that will attempt to document the trophic structure in salt ponds along a salinity gradient to determine how biological processes vary with differing physical regimes and to predict outcomes and consequences of wetland restoration efforts. The broader investigation will include physical measurements that include water depth, wind-waves, pH, specific conductance (salinity), temperature, dissolved oxygen, and suspended solids (turbidity). Also, sediment fluxes will be compared with geomorphic evolution of the sloughs. Biological studies will include primary productivity and nutrient concentrations, variations in diversity (composition and abundance) of invertebrates, fishes, and birds, dietary preferences of fishes and birds, movement of birds, and the interrelationship of these components.

For this subtask, fish and water quality data were collected from at least four salt ponds containing salinities that are likely to support fish life (0-60 parts per thousand). Sample collections occurred at bimonthly intervals during 1999-2000. Fish were sampled with gill nets, seines, and other appropriate gear. Water quality was measured with a Hydrolab DataSonde 3 multiprobe. Fish were identified and counted, then the first 25 individuals of each species was measured for standard length and weighed. In addition, as many as 25 individuals of selected fish species were preserved in 10% formalin for gut analysis. The gut analysis was conducted with standard procedures that quantify the relative importance (wet weight basis) of various forage categories. Multivariate statistical procedures will be used to identify the environmental variables that most influence distribution and composition of fishes inhabiting the salt ponds.

Highlights and Key Findings

During July 1999-September 2000, a total of 3,976 fish representing 16 species was captured from Ponds 1, 2, and 3. Gillnetting yielded 685 fish (17.2%) whereas bag seining yielded 3,291 fish (82.8%). Judging from gill net catches, fish abundance was high in both Pond 1 (323 fish) and Pond 2 (343 fish), with far fewer fish captured in Pond 3 (19 fish). No fish were captured in Pond 4. By comparison, bag seine catches indicated that fish abundance was highest in Pond 1 (2,559 fish), followed by Pond 3 (617 fish), and then by Pond 2 (115 fish). As with gillnetting, bag seining failed to capture fish in Pond 4. Gillnetting and bag seining sampled different segments of the fish species assemblage in each pond. In Pond 1, gill nets captured mostly American shad (38.4%), striped bass (41.2%), and striped mullet (9.0%) whereas bag seines captured mostly Pacific staghorn sculpin (51.8%) and yellowfin goby (41.2%). In Pond 2, gill net catches consisted almost exclusively of striped bass (95.0%) whereas bag seine catches consisted mostly of inland silverside (49.6%) and striped bass (39.1%). In Pond 3, gill nets captured striped bass (47.4%), longjaw mudsucker (36.8%), and yellowfin goby (15.8%), whereas bag seines captured mostly longjaw mudsucker (56.2%), chameleon goby (26.1%), and inland silverside (11.2%). Gut analysis of representative fish species from Ponds 1-3 are still in progress. Except for temperature, which averaged 15.5-20.1 C, water quality conditions varied significantly among the four ponds (Table 2). Mean concentrations of dissolved oxygen were similar in Ponds 1, 2, and 3 (6.9-8.0 mg/L) but considerably lower in Pond 4 (1.6 mg/L). On average, pH values differed significantly between Pond 2 (8.6) and Pond 4 (7.5). However, mean pH values in Ponds 1 and 3 (7.9-8.3) did not differ significantly from values measured in the other two ponds. Mean salinity concentrations varied among ponds, with similar concentrations occurring in Pond 1 (23.7 parts per thousand; ppt) and Pond 2 (24.9 ppt), but progressively higher concentrations occurring in Pond 3 (43.8 ppt), and Pond 4 (>70 ppt). Finally, mean turbidity levels were similar among Ponds 2-4 (36.4-60.6 NTUs) and significantly higher in Pond 1 (139.9 NTUs). In early March 2002, the Humboldt State University graduate student assigned to this project indicated that he was no longer interested in completing his thesis project due to other business commitments. Field notes and other raw data, plus unanalyzed fish-gut samples, were transported to the WFRC-Dixon Duty Station in late March. We are attempting to hire a technician to complete analysis of samples, with data interpretation and writeup now scheduled to begin in late summer or fall.

Where Are We Headed In 2003

Field work for this study has been completed. If additional USGS Place-based Program (cyclical) funds are received, we will complete fish gut analyses and data entry into computer spreadsheets, and initiate statistical analysis and interpretation of fish-catch and gut contents. If cyclical funds are not received, we will statistically analyze and interprete only the fish-catch data set.

Project Contact

Michael Saiki
U.S. Geological Survey
Western Fisheries Research Center
Dixon Duty Station
6924 Tremont Road
Dixon, CA 95620-9648

Email: mike_saiki@usgs.gov
Phone: 707-678-0682 x617
Fax: 707-678-5039

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