We used monthly otter trawling and beach seining to sample the fishes of Suisun Marsh in the San Francisco Estuary from 1979 to 1999. We collected nearly 173,000 fish, mostly young of the year, representing 28 native species and 25 alien species. Catch data were related to temperature, salinity, water transparency, and several measures of freshwater inflow into the marsh. Species abundance and distribution within the marsh were the product of several interacting factors:(1) the timing and place of reproduction of the abundant resident species, (2) past reproductive success, (3) habitat differences among sloughs, and (4) physiological tolerance. We did not find consistent groups of potentially interacting species, although some native species showed weak concordance in abundance. The lack of persistent fish assemblages is related to the naturally fluctuating environmental conditions of the estuary, the overall decline in fish abundance through time, and the frequent invasions of alien fishes and invertebrates. Our results suggest that the fish assemblages in Suisun Marsh will continue to be unpredictable until estuarine processes approach their historic range of variability and alien invasions are halted.

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We sampled ichthyoplankton weekly in Suisun Marsh in the San Francisco Estuary from February to June each year from 1994 to 1999. We collected approximately 227,900 fish, predominantly shimofuri goby Tridentiger bifasciatus (60%) and prickly sculpin Cottus asper (33%). Principal components analysis and canonical correspondence analysis were used to explore relationships among several environmental variables and the 13 species that made up 99.96% of the catch. A group of native fishes (prickly sculpin, Sacramento sucker Catostomus occidentalis, threespine stickleback Gasterosteus aculeatus, longfin smelt Spirinchus thaleichthys, and Sacramento splittail (also known simply as splittail) Pogonichthys macrolepidotus) were associated with the cool temperatures and higher outflows characterizing early‐season conditions in Suisun Marsh. In contrast, a group of introduced species (shimofuri goby, inland silverside Menidia beryllina, striped bass Morone saxatilis, and threadfin shad Dorosoma petenense) were associated with the warm temperatures and lower outflows that characterize late‐season marsh conditions. Catch composition was similar among marsh waterways (called sloughs), except for Cordelia Slough in the western marsh, which had lower total catch, greater diversity, and most of the threespine stickleback, northern anchovy Engraulis mordax, and longfin smelt. Longfin smelt were captured mostly in February and March, whereas delta smelt Hypomesus transpacificus catches were later and more evenly distributed throughout the marsh. Delta smelt catches overlapped temporally and spatially with catches of the introduced wakasagi H. nipponensis. Sacramento splittail catches were confined mostly to 1995, a year when high flows peaked during their spawning season in March and April. Our results suggest that temperature and interannual variations in freshwater flow are important for determining habitat quality for native and introduced larval fishes. We conclude that mimicking natural flow regimes in this highly regulated system is important for early life stages of native fishes.

SynopsisWe documented species7 distributions, size structure of populations, abundance in mainstem and tributary streams, habitat use, and diets of prickly sculpin, Cottus asper, and coastrange sculpin, C. aleuticus, in the Eel River drainage of California, to determine the processes allowing coexistence of these very similar fishes. We observed prickly sculpins at 43 sites and coastrange sculpins at 34. The species co-occurred at 26 sites. Youngof-year coastrange sculpins were only observed within 42 km of the ocean, but young-of-year prickly sculpins were present throughout the species range. Mean, maximum, and minimum lengths of coastrange sculpins were positively correlated with distance from the ocean but no significant relationships were found for prickly sculpins. Absolute abundance of both species was highest in mainstem habitat (prickly sculpins = 0.6 sculpins m-2 and coastrange sculpins = 0.4 sculpins m-'). Tributary densities of both species tended to be less than 0.1 sculpins m-' . The species inhabited very similar habitats and had very similar diets. Coastrange sculpin populations in upstream areas were maintained by immigration from downstream areas in contrast with prickly sculpin populations that produced young-of-year fish throughout their range. Densities were probably not high enough for interspecific interactions to be important. The factors limiting the upstream distribution of the species may include high water temperatures, stability of the stream bed, and behavior of the fish. In the past, the range of sculpins within the Eel River drainage probably fluctuated with changing physical conditions. Recent introductions of exotic species that compete with and prey upon'sculpins, and ongoing human activities in the drainage could result in major reductions in the distribution and abundance of one or both species.