Temperature increases due to climate change over the coming century will likely affect smallmouth bass (Micropterus dolomieu) growth in lotic systems at the southern extent of their native range. However, the thermal response of a stream to warming climate conditions could be affected by the flow regime of each stream, mitigating the effects on smallmouth bass populations. We developed bioenergetics models to compare change in smallmouth bass growth rate potential (GRP) from present to future projected monthly stream temperatures across two flow regimes: runoff and groundwater-dominated. Seasonal differences in GRP between stream types were then compared. The models were developed for fourteen streams within the Ozark–Ouachita Interior Highlands in Arkansas, Oklahoma and Missouri, USA, which contain smallmouth bass. In our simulations, smallmouth bass mean GRP during summer months decreased by 0.005 g g⁻¹ day⁻¹ in runoff streams and 0.002 g g⁻¹ day⁻¹ in groundwater streams by the end of century. Mean GRP during winter, fall and early spring increased under future climate conditions within both stream types (e.g., 0.00019 g g⁻¹ day⁻¹ in runoff and 0.0014 g g⁻¹ day⁻¹ in groundwater streams in spring months). We found significant differences in change in GRP between runoff and groundwater streams in three seasons in end-of-century simulations (spring, summer and fall). Potential differences in stream temperature across flow regimes could be an important habitat component to consider when investigating effects of climate change as fishes from various flow regimes that are relatively close geographically could be affected differently by warming climate conditions.