Aquatic mesocosm studies are being used to refute a presumption of risk derived from laboratory toxicity tests conducted under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA). Mesocosm studies incorporate many biological, chemical, and physical characteristics of natural ecosystems. Hence, they serve as realistic surrogates of natural ecosystems and allow tests of pesticide effect at the population, community, and ecosystem level. We discuss two factors, ecosystem trophic status and organism life history, which influence the results derived from aquatic mesocosm studies. Trophic status influences the fate and effects of chemicals which strongly sorb or biologically degrade, yet may not be as important in the fate and effects of more water soluble chemicals. Life history traits of organisms and the intensity, frequency, and duration of the pesticide disturbance also determine the mesocosm response pattern.