Animal communities play significant roles in the processing of organic matter and nutrient cycling within lentic and lotic ecosystems. One of the most overwhelming tasks associated with assessing the impact of pesticides in ecosystems is that of assessing the indirect effects that result from the direct effects of pesticides on the biota. Because all functional groups do not respond similarly to pesticide treatments, changes in functional community structure and production can alter drastically ecosystem-level phenomenona such as energy flow, food chains, nutrient cycles, and heterotrophic “regulation” (cybernetics) within the ecosystem. Some specific examples of indirect effects of pesticides on aquatic ecosystems are given. There are definite needs for mesocosm and ecosystem-level testing of pesticides; however, at the same time we need to ask the following question: How applicable are the results obtained from one freshwater system to another? Too few comparative studies of aquatic ecosystems exist to make broad sweeping generalizations between various regions, which differ in abiotic and biotic characteristics. More comparative studies of freshwater ecosystems are sorely needed. Manipulations of ecosystems, which include applications of pesticides, can contribute substantially to our knowledge of ecosystem structure and function; however, the researchers must have a good working knowledge of the particular ecosystem before such treatments. Before system-level manipulations are made several questions should be asked, which should enable researchers to formulate predictions and design experiments that key in on ecosystem processes that may be influenced by pesticides.