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A hybrid model was used to characterize potential ecological risks posed by atrazine to the endangered Topeka shiner. The model linked a Topeka shiner individual-based bioenergetics population model (TS-IBM) to a comprehensive aquatic system model (CASM TS ) to simulate Topeka shiner population and food web dynamics for an Iowa (USA) headwater pool. Risks were estimated for monitored concentrations in Iowa, Missouri, and Nebraska (USA), and for monitored concentrations multiplied by 2, 4, and 5. Constant daily atrazine concentrations of 10, 50, 100, and 250 µg/L were assessed. Exposure-response functions were developed from published atrazine toxicity data (median effect concentrations [EC50s] and no-observed-effect concentrations). Two toxicity scenarios were developed: the first included sensitive and insensitive species of algae, and the second reduced algal EC50 values to increase atrazine sensitivity. Direct and indirect effects of atrazine on Topeka shiner prey were modeled; direct effects on Topeka shiner were not assessed. Risks were characterized as differences between population biomass values of 365-d baseline and exposure simulations. The results indicated no discernable food web effects for monitored atrazine concentrations or constant exposures of 10 µg/L on Topeka shiner populations for either toxicity scenario. Magnified monitored concentrations and higher constant concentrations produced greater modeled indirect effects on Topeka shiners. The hybrid model transparently combines species-specific and surrogate species data to estimate food web responses to environmental stressors. The model is readily updated by new data and is adaptable to other species and ecosystems. Environ Toxicol Chem 2019;38:2243-2258. © 2019 SETAC., (© 2019 SETAC.)