A method to characterize and statistically analyze size distributions was developed and the response of size distributions to experimental manipulations was investigated. Four pond and mesocosm experiments were used to examine the effects of various factors, including nutrient loading, piscivorous fish, consumer fish, and toxicants, on pelagic and benthic size distributions. Size distributions were used to quantify benthic-pelagic linkage and to compare the relative response of each habitat to the treatments. Changes in the N:P ratio with body size were also quantified with size distributions, as well as the ability of planktivorous fish to alter the N:P ratio in the pelagic habitat.