In this study, we continuously observed water temperatures in the main irrigation canal and the main branch and farm drains of a paddy area with independent irrigation and drainage canals. We focused on the flow-down pathway that changes with various water management practices. As a result, we found that the maximum temperature in the farm drain was higher in July than in August, a trend similar to reported temperature changes of water stored in paddy plots. It appears that water temperature in the farm drain strongly reflects paddy outflow. At drainage canals, water temperature was reduced in July and rose in August. Our findings clarified that water temperature changed in the drainage canal not only because of heat exchange due to weather conditions but also because of inflow from the irrigation canal and outflow from the paddy plots. This study provides evidence for the strong impact of water management on paddy area water temperatures with independent irrigation and drainage canal settings, as farmers control the amount of inflow from irrigation canals and outflow from drainage water, depending on the stage of growth and weather conditions.