Stormwater control measures (SCMs) have been employed to mitigate peak flows and pollutants ssociated with watershed urbanization. Downstream ecological effects caused by the implementation of SCMs are largely unknown, especially at the watershed scale. Knowledge of these effects could help with setting goals for and targeting locations of local restoration efforts. Unfortunately, studies such as these typically require a high level of time and effort for the investigating party, of which resources are often limited. This study proposes a low-cost investigation method for the prediction of ecological effects on the watershed scale with the implementation of rain garden systems by using publicly available data and software. For demonstration purposes, a typical urban watershed was modeled using Storm Water Management Model (SWMM) 5.0. Forty-five models were developed in which the percent impervious area was varied 3 to 80%, and the fraction of rain gardens implemented with respect to the number of structures was varied from to 100%. The river chub fish (Nocomis micropogon) and its congeners (Nocomis spp.) were chosen as ecological indicators, as they are considered to be keystone species through interspecific nesting association. Depth and velocity criteria for successful nest building locations of the river chub were determined; these criteria can then be applied to many other watersheds. In this study, both base flow conditions and a typical summer storm event (1.3 cm, 6 h duration) were evaluated. During the simulated storm, nest-building locations were not affected in the 3 and 5% impervious cover models. Nest destruction was found to occur in approximately 54% of the original nest building sites for the 9% and 10% impervious areas. Nearly all of the nest-building locations were uninhabitable for impervious areas 20% and greater. Rain garden implementation significantly improved river chub habitat in the simulation, with greatest marginal benefit at lower levels of implementation.