We measured the size structure and taxonomic composition of phytoplankton in temperate rivers during base flows of summer to investigate the influence of river size, ambient nutrient concentration, and light availability on potamoplankton community structure. Algal biomass was measured in three size classes (2–20, 20–64, and >64 µm) by microscope enumeration of water samples collected in 31 rivers and by chlorophyll a in water samples collected in 46 rivers in another year across Ontario and western Quebec. Nanoplankton dominated the potamoplankton biomass across the range of river nutrient concentrations (total phosphorus 5–280 µg P L−1), water residence times (1–39 d), and light regimes (euphotic zone to mixing depth ratio 0.1–33). Both nanoplankton (2–20 µm) and total potamoplankton biomass were significantly correlated with water column total phosphorus concentrations and were not related to water residence time or light availability. On average, diatoms contributed the largest percentage of the total biomass, followed by cryptophytes and an equal percentage of chlorophytes and chrysophytes. The contribution of any one division to total biomass was not significantly correlated with nutrients, water residence time, or light regime. In contrast to temperate lake systems, both the proportion of biomass in larger size classes and the contribution of cyanobacteria did not change significantly as a function of nutrient concentrations. However, community size structure varied in relation to river size: netplankton (>64 µm) contributed slightly more to total biomass at sites with both shorter (<2 d) and longer (>10 d) water residence times. These results point to differences between the phytoplankton of lakes and rivers in response to eutrophication.