Dual‐labeling assays were performed on the phytoplankton community of Lake Biwa (Japan) to estimate the ratio of inorganic carbon to nitrate‐N uptake as a function of cell size and irradiance. The assays were conducted during a period of change in underwater light and phytoplankton species composition associated with typhoon‐induced mixing events. There were consistent qualitative differences in the C:N uptake characteristics of large (>2 µm) versus small (<2 µm) phytoplankton. For both fractions, the ratio of C:N uptake versus irradiance was well described by a log‐log model; however, in the majority of assays, the slope of the relationship was positive for the >2‐µm fraction and negative for the small cells. This striking difference between the two fractions also corresponded to patterns in the C:N stoichiometry of the plankton. Surface samples of the >2‐µm fraction had a higher C:N ratio than deep populations; this pattern was not seen in the <2‐µm seston. Similarly, a decrease in water‐column transparency associated with the typhoon events was accompanied by a significant correlative trend of increasing C:N ratios in the <2‐µm fraction and decreasing C:N ratios in the >2‐µm fraction. These observations imply that in aquatic ecosystems where nitrate plays an important role in the nitrogen economy of the phytoplankton, high‐irradiance conditions favor maximum biomass production per unit of nitrogen uptake by large phytoplankton, and low‐irradiance conditions favor a high biomass increment per unit of nitrogen uptake by small cells. These observations are consistent with the ecological distribution of large‐ versus small‐cell phytoplankton in several types of freshwater and marine environments.