Predicted impacts of climate change in the eastern United States are pervasive and complex, including increased precipitation and frequency of heavy precipitation events, and altered seasonality of rainfall. This will potentially lead to increased flooding frequency and severity. The River Chub Nocomis micropogon is an important keystone and engineer species in the eastern United States, primarily through its construction of nesting habitat which is shared with other species (‘nest associates’) in a mutualistic relationship. River Chub nests are vulnerable to high flows caused by excessive precipitation and by urbanization of watersheds. Published thresholds linking River Chub nest disruption with stream discharge were used to interpret fine‐ scale predictions of a downscaled climate prediction model (HadGEM2‐ES), using a stochastic weather generator (LARS‐WG6) calibrated to two climate change scenarios. This was examined for a case study watershed, Big Elk Creek, in Maryland. The amount of River Chub nest disruption was compared between present day stream discharge observations (2010‐ 2021) and simulated data for 2061‐ 2080 under the ‘worst‐case’ RCP85 and the ‘probable‐ case’ RCP45 scenarios. Significantly elevated nest disruption under both RCP45 and RCP85 scenarios over observed current conditions was found under status quo watershed characteristics in the form of more disruptive events, more disrupted days, and shorter disruption‐ free days during the River Chub nesting season. Increased nest disruption projected by the downscaled HadGEM2‐ES climate prediction model was moderate, and far below the level of nest disruption observed in flashy urbanized streams that have lost or may have lost River Chub populations in the region. The moderate impacts of increased flooding from climate change will interact with projected growth in population and urbanization projected for the Big Elk Creek watershed. Mechanistic modeling of fine‐ scale processes using stochastic weather generators shows promise in modeling responses of ecosystems to changing conditions.