Early Life History of Fishes in the San Francisco Estuary and Watershed

<em>Abstract.</em>—In July 2000 and 2001, we sampled adjacent screened and unscreened agricultural irrigation diversions in the Sacramento River, California to (1) evaluate the effectiveness of a custom fish screen for excluding four open-water fishes: native delta smelt <em>Hypomesus transpacificus </em>and alien threadfin shad <em>Dorosoma petenense</em>, inland silverside <em>Menidia beryllina</em>, and striped bass <em>Morone saxatilis</em>; and (2) examine factors affecting entrainment of each species. We also compiled trawl and beach seine data from contemporaneous monitoring programs to make inferences about microhabitat use by these fishes and its implications for entrainment vulnerability. The fish screen reduced entrainment of each species by 99% or more and excluded many fish less than 25 mm, the approximate minimum length it was designed to exclude. Tidal and diel influences on entrainment through the unscreened diversion were observed, but diel cycles appeared to be more important, as most entrainment occurred at night or during crepuscular periods. Except for delta smelt, our results suggested that open-water fishes may undergo ontogenetic changes in vulnerability to unscreened irrigation diversions. Fishes entrained during daylight (threadfin shad and striped bass) averaged only 15–16 mm in length. At night, average lengths of entrained threadfin shad and inland silverside were 22–25 mm, even though larvae continued to be entrained. Similarly, a diel influence on striped bass entrainment was observed only in 2000, when individuals larger than 20 mm were consistently collected. No striped bass were collected at sizes greater than 35 mm, even though larger individuals occupied the study area. We found no evidence of size-related changes in delta smelt vulnerability to entrainment, but the monitoring data indicated that delta smelt were abundant offshore, whereas the other three species were most abundant nearshore. We think that low and inconsistent entrainment of delta smelt reflected (1) predominantly offshore habitat use by delta smelt, and (2) the relatively small hydrodynamic influence of the diversion.