The use of complex microcosms as tools for testing mathematical models of pollutant fate was evaluated by determining the transport and transformation of methyl parathion in two-8-compartment, continuous flow microcosms designed to enhance the effects of different degradation processes. Objectives were to develop different chemical and biological environments by adding inorganic nutrients, glycerol, contrived sediments, and natural sediments sequentially to compartments down the length of the channel; to determine whether the microcosms established stable states during the experimental periods; and to determine whether the fate of methyl parathion was related to environmental characteristics of each compartment. Observed differences in chemical treatments were reflected by differences in community structure and community function. Statistical comparisons of bacterial and total microbial biomass revealed significant differences; compartments with organic and inorganic nutrient additions were generally grouped separately from those with only inorganic nutrient additions. Relative rates of diurnal dissolved oxygen change were also significantly different between those compartments with different nutrient additions. Inclusion of natural and contrived sediments had few significant effects on the structure or function of the water or aufwuchs communities.