Water management is increasingly important for rice productivity to maintain soil temperature and fertility with the presence of global warming. Meanwhile, rice production in Japan is in urgent need to reduce the costs through improving the efficiency and market competitiveness. This paper aims to measure effect of water depth and water temperature on rice yield of individual paddy fields and improve the practice of water management for them. In the first stage, we measure the production efficiency of rice yield through the adoption of data envelopment analysis. The results indicate that enlarged scale of the paddy fields increases the efficiency, and rice quality can be improved more than quantity. Moreover, the most inefficiently used inputs include the amount of fertilizer nitrogen and the soil capacity, which is a compound measurement of 21 soil chemical properties. In the second stage, after comparing the 20 paddy fields with highest and lowest technical efficiency, an observation shows that the rice yield is much more affected by water temperature than by water depth. The data of all the variables used in this study were sampled in 2015 and comprised of 110 paddy fields of Koshihikari, one of the most popular Japanese rice varieties, from a large-scale farm located in Kanto Region of Japan. In the analysis, the outputs include yields of raw paddy, paddy with 15% moisture, unsorted brown rice, sorted brown rice, milled grain rice, and perfect grain rice. The inputs include the field area, air temperature, solar radiation, fertilizer nitrogen, soil capacity, and farming conditions.