<em>Abstract.</em>—We examined assemblage patterns of early life stages of fishes for two major tributaries of the upper San Francisco Estuary: (1) Sacramento River channel, and (2) Yolo Bypass, the river’s seasonal floodplain. Over four hydrologically diverse years (1999–2002), we collected 15 species in Yolo Bypass egg and larval samples, 18 species in Yolo Bypass rotary screw trap samples, and 10 species in Sacramento River egg and larval samples. Fishes captured included federally listed species (delta smelt <em>Hypomesus transpacificus </em>and splittail <em>Pogonichthys macrolepidotus</em>) and several game species (American shad <em>Alosa sapidissima</em>, striped bass <em>Morone saxatilis</em>, crappie <em>Pomoxis </em>spp., and Chinook salmon <em>Oncorhynchus tshawytscha</em>). As in other regions of the estuary, alien fish comprised a large portion of the individuals collected in Yolo Bypass (40–93% for egg and larval net samples; 84–98% for rotary screw trap samples) and Sacramento River (80–99% for egg and larval net samples). Overall ranks of species abundances were significantly correlated for Yolo Bypass and Sacramento River, suggesting that each assemblage was controlled by similar major environmental factors. However, species diversity and richness were higher in Yolo Bypass, likely because of a wider variety of habitat types and greater hydrologic variation in the floodplain. In both landscapes, we found evidence that timing of occurrence of native fishes was earlier than aliens, consistent with their life history and our data on adult migration patterns. We hypothesize that Yolo Bypass favors native fishes because the inundation of seasonal floodplain typically occurs early in the calendar year, providing access to vast areas of spawning and rearing habitat with an enhanced food web. Conclusions from this analysis have implications for the management of aquatic biodiversity of tributaries to the San Francisco Estuary and perhaps to other lowland rivers.
Enumeration of Juvenile Salmonids in the Okanogan Basin Using Rotary Screw Traps, Performance Period: March 15, 2006 - July 15, 2006.