The ecotoxic effects of atrazine (0, 20, 100, and 500 μg/l exposure rates) on experimental pond mesocosm ecosystems were evaluated after 805 days of continuous exposure. Analysis of data was done using LISREL, a structural equation modeling technique. A series of five ecosystem models were developed with LISREL with each model including a unique subset of macroinvertebrate concepts. All models identified both direct and indirect effects of the exogenous concepts (grass carp, pond depth, and atrazine) on all endogenous concepts (i.e., fish, aquatic vegetation, phytoplankton, zooplankton, and macroinvertebrate concepts). All models quantify the ecotoxic effects (direct and indirect) of atrazine on the various endogenous concepts (structural units of these ecosystems) by specifying the functional paths that connect them. Direct ecotoxic effects of atrazine were primarily limited to reductions in gizzard shad biomass and aquatic vegetation abundance (% cover). Most indirect effects associated with atrazine exposure were initiated by atrazine’s direct effect on the aquatic plant community. Measures of the direct, indirect, and total effects of atrazine on affected endogenous concepts are provided and the ecological consequences of these effects are discussed.