Algal chlorophyll, carbon fixation and alkaline phosphatase activity were net-fractionated using 22-μm, and 75-μm screens in three lakes with contrasting zooplankton communities. Size distributions of algal biovolume were also determined through microscopic examination. Relatively good correspondence was found between size distributions obtained through net fractionation and those determined by microscopic examination. Biovolume-specific carbon fixation and chlorophyll decreased with increasing fraction size but no differences were observed among fractions for chlorophyll-specific carbon fixation. High algal standing stocks and low phosphorus deficiency in Tuesday Lake were attributed to low grazing pressure by small, inefficient zooplankton and possible limitation by nutrients other than phosphorus. Algal standing stocks were low and phosphorus deficiency was high in Peter and Paul Lakes, in which the zooplankton was dominated by large grazers. Different algal size fractions experienced differing degrees of phosphorus deficiency. These size fraction differences in P-deficiency in Peter and Paul Lakes were attributed to differences in algal species composition and to differing levels of zooplankton grazing pressure and nutrient regeneration. A unimodal relationship between relative nanoplankton biovolume and zooplankton biomass was found and reflects the positive (nutrient regeneration) and negative (grazing mortality) effects of zooplankton on the algal community.