AbstractPotential toxic effects of thiamethoxam on nontarget organisms and the community structure of a generic Midwestern farm pond and emergent wetland were assessed using 2 versions of the comprehensive aquatic system model: CASMGFP, a generic farm pond model, and CASMGWL, a generic wetland model. The CASMGFP and CASMGWL are integrated bioenergetics‐based and habitat quality models that describe the daily biomass values of selected producer and consumer populations representative of generalized Midwestern farm ponds and emergent wetlands. The CASMGFP demonstrated the ability to reproduce values of population biomass reported for Midwestern (and other) pond ecosystems; the CASMGWL provided a similar modeling capability for Midwestern emergent wetlands. Lethal and sublethal effects of thiamethoxam were modeled as extrapolations of laboratory toxicity assays using the CASMGFP and the CASMGWL. Time series of daily environmental concentrations of thiamethoxam constructed for 6 regional pesticide applications across the United States failed to produce any calculated impacts on modeled population biomass or changes in community structure of modeled trophic guilds in the CASMGFP or the CASMGWL. However, evaluation of systematically increased daily concentrations demonstrated the ability of both models to simulate direct and indirect toxic effects of this pesticide. The present model study suggests that process‐based food web/ecosystem models can be used to characterize the potential ecological effects of thiamethoxam on generalized farm pond and emergent wetland ecosystems. Environ Toxicol Chem 2018;37:738–754. © 2017 SETAC