A water temperature simulation model was developed to estimate the effects of water management on the thermal environment in rice paddies. The model was based on two energy balance equations: for the ground and for the vegetation, and considered the water layer and changes in the aerodynamic properties of its surface with water depth. The model was examined with field experiments for water depths of 0 mm (drained conditions) and 100 mm (flooded condition) at two locations. Daily mean water temperatures in the flooded condition were mostly higher than in the drained condition in both locations, and the maximum difference reached 2.6°C. This difference was mainly caused by the difference in surface roughness of the ground. Heat exchange by free convection played an important role in determining water temperature. From the model simulation, the temperature difference between drained and flooded conditions was more apparent under low air temperature and small leaf area index conditions; the maximum difference reached 3°C. Most of this difference occurred when the range of water depth was lower than 50 mm. The season‐long variation in modeled water temperature showed good agreement with an observation data set from rice paddies with various rice‐growing seasons, for a diverse range of water depths (root mean square error of 0.8–1.0°C). The proposed model can estimate water temperature for a given water depth, irrigation, and drainage conditions, which will improve our understanding of the effect of water management on plant growth and greenhouse gas emissions through the thermal environment of rice paddies.