Temporal and spatial temperature distribution in flow regime is vital for the survival of aquatic biota. As Water Source Heat Pump System (WSHP) is gaining wider application, especially in regions with abundant water resources, water discharge of the WSHP system may induce pollution to river flow regime, which may lead to the outbreak of blue-green algae and consequently threaten the survival of other hydrobios. While the characteristics of thermal discharge into seashore and stagnant waterbody are widely investigated, the thermal impact pattern of WSHP to river flow is less acknowledged. Therefore, this paper studies this phenomenon. This paper used numerical simulations to obtain spatial temperature characteristics of the thermal impact zone of a case study of WSHP system’s water discharged into river flow for three worst-case scenarios. For both warm and cold discharge, the shallow water regime is found to be the most affected zone. The water body that sustains temperature difference of 1°C extends about 5m for warm discharge and 2m for cold discharge in depth. However, this zone extends along the riverbank about 80m for warm discharge and 4260 m for cold discharge. This paper introduces a procedure for a preliminary assessment of how the thermal discharge from WSHP systems might threaten the freshwater fishes from a spatial point of view, and this may be a starting point of achieving the microscopic understanding or forecasting of thermal impact of anthropogenic thermal discharge to river flows. This work is fundamental to improve the strategic decisions on WSHP system’s design and operation.