Changes in the size structure of photoautotrophs influence food web structure and the biogeochemical cycling of carbon. Decreases in the median size of diatoms within communities, in concert with climate warming and water column stratification, have been observed over the Cenozoic in the ocean and over the last 50 years in Lake Tahoe. Decreases in the proportion of larger plankton are frequently observed in response to reduced concentrations of limiting nutrients in marine systems and large stratified lakes. By contrast, we show a decrease in the median size of planktonic diatoms in response to higher nutrient concentrations in a set of intermediate-sized alkaline lakes. Climate-induced increases in the frequency, duration and strength of water column stratification may select smaller planktonic species in the ocean and larger lakes owing to a reduction in nutrient availability and sinking rates, while light limitation, stimulated by nutrient eutrophication and high chlorophyll concentrations, may select smaller species within a community owing to their high light absorption efficiencies and lower sinking rates. The relative importance of different physiological and ecological rates and processes on the size structure of communities varies in different aquatic systems owing to varying combinations of abiotic and biotic constraints.