Seasonally variable freshwater flows are known to influence estuarine plankton assemblages. There has been little recent study of the plankton dynamics of the Columbia River Estuary (CRE), a large, river-dominated estuary that has experienced great modification to its hydrological cycle. Zooplankton (>75 mu m) were collected during four late spring (high-flow) cruises and three late summer (low-flow) cruises in 2005 and 2006. Surface-water microplankton (5-200 mu m) were collected during cruises in 2005. Zooplankton and phytoplankton assemblage composition varied along an axial salinity gradient and between flow periods. Estuarine zooplankton were strongly seasonal and dominated by the calanoid copepod Eurytemora affinis in the late spring, high-flow period and by the invasive calanoid Pseudodiaptomus forbesi in the late summer, low-flow period. The phytoplankton assemblage was dominated by freshwater diatoms, primarily Aulacoseira spp. The ciliate Mesodinium rubrum (=Myrionecta rubra) reached high densities during the low-flow period, but otherwise, distinct high-flow and low-flow phytoplankton assemblages were not detected. Comparison to prior studies in the CRE suggests that the plankton assemblage composition during the low-flow period has undergone considerable change, which may in turn have important trophic implications.