Coupled groundwater flow and heat transport within hyporheic zones extensively affect water, energy, and solute exchange with surrounding sediments. The local and cumulative implications of this tightly coupled process strongly depend on characteristics of drivers (i.e., discharge and temperature of the water column) and modulators (i.e., hydraulic and thermal properties of the sediment). With this in mind, we perform a systematic numerical analysis of hyporheic responses to understand how the temporal variability of river discharge and temperature affect flow and heat transport within hyporheic zones. We identify typical time series of river discharge and temperature from gauging stations along the headwater region of Mississippi River Basin, which are characterized by different degrees of flow alteration, to drive a physics‐based model of the hyporheic exchange process. Our modeling results indicate that coupled groundwater flow and heat transport significantly affects the dynamic response of hyporheic zones, resulting in substantial differences in exchange rates and characteristic time scales of hyporheic exchange processes. We also find that the hyporheic zone dampens river temperature fluctuations increasingly with higher frequency of temperature fluctuations. This dampening effect depends on the system transport time scale and characteristics of river discharge and temperature variability. Furthermore, our results reveal that the flow alteration reduces the potential of hyporheic zones to act as a temperature buffer and hinders denitrification within hyporheic zones. These results have significant implications for understanding the drivers of local variability in hyporheic exchange and the implications for the development of thermal refugia and ecosystem functioning in hyporheic zones.