We test the hypothesis that phytoplankton biomass decrease upon entry into the St. Lawrence River from headwaters in Lake Ontario is attributable to a range of causal factors including, decreased photosynthetic fitness due to turbulence, cell loss due to increased flocculation and subsequent sedimentation, decreases in nutrients, and loss due to grazing. In order to test this, changes in phytoplankton and crustacean zooplankton concentrations were examined during four transects along the river, from 8 km offshore in Lake Ontario to the hydroelectric power dam 180 km downstream. Both phytoplankton biomass, measured as chlorophyll-a, and zooplankton decreased markedly upon entry of lake water into the river. Phytoplankton community composition and size changed little over the river reach and tended to reflect that in Lake Ontario. Total phosphorus increased with transit of river water downstream despite low tributary inputs of water into this reach of river. Light availability was high, photosynthetic efficiency suggested that phytoplankton were not physiologically stressed during transit in turbulent waters, and there was no direct evidence of flocculation causing sedimentation of phytoplankton. Grazing by the benthic community (filtering insect larvae and dreissenid mussels) is inferred to be a dominant biological factor as is the geomorphology in this reach of the river, which includes large littoral areas, shoals, and reaches of high water velocity that can increase particle contact in the water column with benthic grazers. The findings of this study have a bearing on understanding how changing water levels in a regulated river might alter areas of benthic grazing.