We analyzed data on spring and summertime larval and juvenile fish distribution and abundance in the upper San Francisco Estuary (SFE), California between 1995 and 2001. The upper SFE includes the tidal freshwater areas of the Sacramento-San Joaquin Delta downstream to the euryhaline environment of San Pablo Bay. The sampling period included years with a variety of outflow conditions. Fifty taxa were collected using a larval tow net. Two common native species, delta smelt Hypomesus transpacifucus and longfin smelt Spirinchus thaleichthys, and four common alien taxa, striped bass Morone saxatilis, threadfin shad Dorosoma petenense, gobies of the genus Tridentiger, and yellowfin goby Acanthogobins flavimanus, were selected for detailed analysis. Outflow conditions had a strong influence on the geographic distribution of most of the species, but distribution with respect to the 2 psu isohaline (X2) was not affected. The distribution patterns of delta smelt, longfin smelt, and striped bass were consistent with larvae moving from upstream freshwater spawning areas to down-stream estuarine rearing areas. There were no obvious relationships of outflow with annual abundance indices. Our results support the idea of using X2 as an organizing principle in understanding the ecology of larval fishes in the upper SFE. Additional years of sampling will likely lead to additional insights into the early life history of upper SFE fishes. ?? Copyright by the American Fisheries Society 2004.