The taxonomic composition and biomass of phytoplankton in the San Joaquin River, California, were examined in relation to water depth, flow regime, and water chemistry. Without substantial tributary inflow, maintenance demands exceeded algal production during summer and autumn in this eutrophic, 'lowland type' river due to light-limiting conditions for algal growth. Streamflow from tributaries that drain the Sierra Nevada contributed to a substantial net gain in algal production during the spring and summer by increasing water transparency and the extent of turbulence. Abundances of the major taxa (centric diatoms, pennate diatoms and chlorophytes) indicated differing responses to the longitudinal variation in water depth and flow regime, with the areal extent of pools and other geomorphic features that influence time-for-development being a major contributing factor to the selection of species. Tychoplanktonic species were most abundant upstream and in tributaries that drain the San Joaquin Valley. Seasonally-varying factors such as water temperature that influence algal growth rates also contributed significantly to the selection of species. Nutrient limitation appears not to be a primary constraint on species selection in the phytoplankton of this river.