Abstract Large river estuaries experience multiple anthropogenic stressors. Understanding plankton community dynamics in these estuaries provides insights into the patterns of natural variability and effects of human activity. We undertook a 2-year study in the Columbia River Estuary to assess the potential impacts of abiotic and biotic factors on planktonic community structure over multiple time scales. We measured microplankton and zooplankton abundance, biomass and composition monthly, concurrent with measurements of chlorophyll a, nutrient concentrations, temperature and salinity, from a dock in the lower estuary. We then statistically assessed the associations among the abundances of planktonic groups and environmental and biological factors. During the late spring high ﬂow period of both years, the lower estuary was dominated by freshwater and low salinity-adapted planktonic taxa, and zooplankton grazers were more strongly associated with the autotroph-dominated microplankton assemblage than abiotic factors. During the early winter period of higher salinity and lowerﬂow, nutrient(P) availability exerted a strong inﬂuence on microplankton taxa, while only temperature and upwelling strength were associated with the zooplankton assemblage. Our results indicate that the relative inﬂuence of biotic (grazers) and abiotic (salinity, ﬂow, nutrients and upwelling) factors varies seasonally and inter-annually, and among different size classes in the estuarine food web.