Stream fish assemblages are shaped by natural hydrologic variability, but flow alteration and environmental change can push systems beyond ecological thresholds that trigger rapid shifts in community structure. In stream systems characterized by naturally variable flow regimes, small changes in hydrologic or environmental conditions may result in disproportionate losses of native species and facilitate the establishment of non-native fishes. Understanding where these thresholds occur and how assemblages respond is essential for anticipating community change under ongoing hydrologic modification. We used fish occurrence data from Great Plains streams and integrated these records with hydrologic and environmental variables. Species were classified as native or non-native and assigned to trophic groups. We examined the influence of hydrologic and environmental gradients on assemblage and species level threshold responses using gradient forest. We expect to observe nonlinear shifts in assemblage composition along environmental gradients. Native species occurrence and site-level persistence are anticipated to remain relatively stable across portions of environmental gradients but then decline more abruptly once particular hydrologic or environmental thresholds are exceeded, rather than exhibiting simple linear declines. We also anticipate that the specific position and magnitude of these threshold responses may vary among sites or hydrologic contexts, which would highlight the value of identifying specific benchmarks for management. These results aim to inform fisheries conservation and management strategies focused on maintaining native biodiversity and ecosystem function across hydrologically diverse Great Plains stream ecosystems.