In rivers, water temperature has a significant impact on aquatic organisms. Thermal infrared sensors mounted on unmanned aerial vehicles (UAVs), which can measure surface temperatures over an area with high spatial resolution, provide new ways to investigate river water temperatures. Therefore, we analyzed the high‐spatial‐resolution water temperature distribution acquired by UAV as an environmental factor affecting Calopteryx japonica inhabiting the river. The study site was a 9‐km section of the Sasayama River in the Kako River system, Japan. Adult and larval C. japonicas were counted walking along the water's edge. The water temperature distribution was determined by taking UAV photographs in August, when river temperatures were estimated to be the highest of the year, and in February, when river temperatures were estimated to be the lowest in the study area. The number of adult and larval C. japonicas were used as the objective variable, and water temperature, vegetation, and water area classification were used as variables in RandomForest analysis. These findings are consistent with existing research on C. japonica ecology. The analysis revealed that the water temperature distribution acquired by UAV can be used as an environmental factor in the analysis of aquatic organisms. This method has the potential to be applied to the analysis of other aquatic organisms.