AbstractPermafrost in the Arctic regions is degrading in response to decades of amplified warming. Advanced degradation of ice‐rich permafrost could significantly alter the water balance by increasing runoff and flooding. How do the hydrological changes in river systems, in turn, affect the permafrost thermal state, specifically in floodplains? First, we develop a first‐order heat budget approach to simulate evolving river‐water temperature. The river‐water thermal model includes heat exchanges at both the air‐water and water‐subsurface interfaces and can accurately estimate water temperature. Then, river‐water temperature is employed as an upper boundary condition for the control volume permafrost model, which models the thermal state of shallow permafrost. The combined model is validated and applied in the Kuparuk River floodplain, Alaska. Results indicate that permafrost warms rapidly during inundation and that channelbelt active layer thickness can deepen by more than 1 m. We find that earlier arrival of the spring freshet and associated earlier inundation onset, as well as increase in river discharge, can significantly increase subsurface permafrost temperature and lead to a deepening of the active layer. In recent years Kuparuk River streamflow has arrived earlier, and mean annual river discharge has increased by 35% since the 1970s. New permanent water and seasonal water appeared throughout the river network of the Kuparuk River since the 1980s according to satellite observations. These hydrological changes likely have contributed to the expansion of riverbed thaw bulbs and the degradation of floodplain permafrost.