Temperature differences between the atmosphere and river water allow rivers to be used as a hydrothermal energy source. The river-water heat pump system is a relatively non-invasive renewable energy source; however, effluent discharged from the heat pump can cause downstream temperature changes which may impact sensitive fluvial ecosystems. In this study, the water temperature recovery distance of the effluent was estimated for a river section in the Han River Basin, Korea, using the heat transfer equation and the Environmental Fluid Dynamic Code (EFDC) model. Results showed that, compared to the EFDC model, the heat transfer equation tended to overestimate the water temperature recovery distance due to its simplified assumptions. The water temperature recovery distance could also be used as an objective indicator to decide the reuse of downstream river water. Furthermore, as the river system was found to support an endangered fish species that is sensitive to water environment changes, care should be taken to exclude the habitats of protected species affected by water temperatures within water temperature recovery distance.