Discharge and thermal regimes are widely considered to be among the strongest drivers of ecosystem structure and function in rivers and streams. Both of these drivers are modified by climate change, land use change, and water resource management, creating persistent threats to riverine ecosystems. The field of flow ecology has greatly advanced our understanding of how animals respond to flow alteration, but our ability to predict responses is still limited, in part, due to a lack of understanding of how flow interacts with other variables such as temperature. Jointly considering flow and temperature together can greatly improve our predictions of how organisms respond to global change. We used long-term (26 yr) data of annual count surveys of shoal-dwelling fishes in two biodiverse rivers in the southern Appalachians in GA, USA to test hypotheses of how high and low flows and stream temperature could affect abundances of fishes. We evaluated specific hypotheses for seven species, including one species of high conservation concern, using Bayesian generalized mixed models. We found that high flow events decreased abundances in the current year for all species, but had mixed effects the following year, with three species showing positive responses and three species exhibiting negative responses. A possible mechanism for the lagged positive effect of high flows is improved habitat conditions from flushing of sediment. Low-flow extremes also generally had a negative effect on species abundances in the current year, but less of an effect the following year relative to high-flow events. Warmer water temperatures were negatively correlated with abundances for most species, but there were strong positive effects for one species (Noturus leptacanthus). Our results provide evidence that changes in flow and temperature regimes may impact native fishes in southern Appalachian rivers. Future analyses will include a greater suite of species (22) and consider if historical biogeography (i.e., evolutionary climates) improves predictions of species responses.