We studied the use of size distributions as a response variable in limnological experiments. Previous quantifications of size distributions were incomplete or difficult to use in experimental settings, and we developed a multivariate approach that more fully describes the shape and biomass of planktonic and benthic size distributions. We re-evaluate the hypothesis that fish affect the shape and nutrients affect the biomass of size distributions, and show that the multivariate approach is more responsive to detecting treatment effects. In a mesocosm experiment, we use this new quantification and analysis of size distributions to detect the main and interactive effects of nutrient addition and sediment type on both benthic and pelagic size distributions. Size distributions in both habitats responded to the nutrient and sediment treatments, indicating linkage since a treatment applied in one habitat affected the size distribution in the opposite habitat. Since size distributions reduce each habitat into a common currency, we were able to examine the nature of the linkage. The relative response of each habitat to the nutrient treatment was different with regard to the shape of the distributions, while the relative response to the sediment treatment was different with regard to the biomass in the distributions.