We analyzed data on spring and summertime larval and juvenile fish distribution andabundance in the upper San Francisco Estuary (SFE), California between 1995 and 2001. Theupper SFE includes the tidal freshwater areas of the Sacramento–San Joaquin Delta downstreamto the euryhaline environment of San Pablo Bay. The sampling period included years with avariety of outflow conditions. Fifty taxa were collected using a larval tow net. Two common nativespecies, delta smelt (Hypomesus transpacificus) and longfin smelt (Spirinchus thaleichthys), andfour common alien taxa, striped bass (Morone saxatilis), threadfin shad (Dorosoma petenense),gobies of the genus Tridentiger, and yellowfin goby (Acanthogobius flavimanus), were selectedfor detailed analysis. Outflow conditions had a strong influence on the geographic distribution ofmost of the species, but distribution with respect to the 2 psu isohaline (X2) was not affected. Thedistribution patterns of delta smelt, longfin smelt, and striped bass were consistent with larvaemoving from upstream freshwater spawning areas to downstream estuarine rearing areas. Therewere no obvious relationships of outflow with annual abundance indices. Our results support theidea of using X2 as an organizing principle in understanding the ecology of larval fishes in theupper SFE. Additional years of sampling will likely lead to additional insights into the early lifehistory of upper SFE fishes.