Structural equation modeling with LISREL was applied to the analysis of the effect of atrazine on a pond ecosystem. This ecosystem analysis is a path analytic approach that relies on modeling ecosystem structure and function. Ecosystems can be thought of as a set of compartments, each compartment being a structural component. These structural components were modeled as a series of concepts, each concept indicated by one or more actual variables. Functional relationships between compartments were represented by pathways connecting the compartments. LISREL provides a measure of ecosystem stability, and the total, direct, and indirect effects of all components on all other components. Three models were developed in which the vertebrate structural component of the ecosystem is decomposed into individual species components. A fourth model was developed that reorganizes the smallest compartment model. In general, as models became larger (more components), the ecosystem became more unstable. It was also found that as there was an increase in the number of same-sign direct and indirect effects, i.e., both are positive or both are negative, the ecosystem becomes less stable. Modeling with LISREL provides several insights into how chemical stresses can operate, and we discuss the role of LISREL in ecosystem modeling and ecotoxicological testing.