Abstract.-We examined factors affecting fish entrainment at California's State Water Project and Central Valley Project, two of the largest water diversions in the world. Combined, these diversions from the upper San Francisco Estuary support a large component of the municipal and agricultural infrastructure for California. However, precipitous declines in the abundance of several estuarine fish species, notably the threatened delta smelt Hypomesus transpacificus, have generated major concern about entrainment as a possible cause of the declines. We examined a 13-year data set of export pumping operations and environmental characteristics to determine factors affecting entrainment (as indexed by salvage at fish screens) and the potential for manipulation of these factors to improve conditions for fish. Entrainment of three migratory pelagic species-delta smelt, longfin smelt Spirinchus thaleichthys, and striped bass Morone saxatilis-was primarily determined by the seasonal occurrence of particular life stages close to the export facilities. We also found that the direction and magnitude of flows through the estuary and to the export facilities were reasonable predictors of pelagic fish entrainment. Entrainment of resident demersal species (prickly sculpin Cottus asper and white catfish Ameiurus catus) and littoral species (Mississippi silverside Menidia audens and largemouth bass Micropterus salmoides) was not explained by diversion flows, although large numbers of individuals from these species were collected. Our study suggests that entrainment of pelagic species can be effectively reduced by manipulating system hydrodynamics.