Habitat use by juvenile salmonids in the Smith River estuary, California

Estuaries are highly productive areas that serve as important nursery habitat for many species of fish. Estuaries provide juvenile salmonids Oncorhynchus spp. with foraging habitats, refuge from predators, and areas in which smoltification and orientation for return migrations can occur. Our primary goal was to describe how juvenile salmonids use the Smith River estuary in northern California, a system that is largely devoid of instream cover and the slough habitat it once contained. The presence of juvenile salmonids was quantified through direct observation (snorkel surveys) and calculations of relative densities in the midchannel and stream margin habitats of the estuary. We completed a total of 755 dives between May 1999 and November 2000. We found that significant differences existed between the relative densities of juvenile Chinook salmon O. tshawytscha and trout (coastal cutthroat trout O. clarkii clarkii and steelhead O. mykiss) observed in habitats with and without cover along stream margins. Stepwise logistic analysis was used to correlate the presence or absence of Chinook salmon and trout to stream reach, habitat type, flow (m(3)/s), salinity (%o), temperature (degrees C), and depth (m). In general, juvenile salmonids appeared to preferentially use habitats with overhanging riparian vegetation. However, Chinook salmon presence was most correlated with areas of low salinity (<5%o), while trout presence was most influenced by habitat type. Trout were present most often in stream margin habitats, regardless of other physical factors. Our study demonstrates that riparian vegetation may be an essential component of juvenile salmonid rearing habitat in estuaries with little instream cover.