The high water demand of rice cultivation is mainly due to flood irrigation, which requires large volumes not only to meet evapotranspiration needs, but also due to losses from percolation, lateral seepage, and surface runoff. In addition to lowering water use efficiency, surface runoff may transport nutrients. This study aimed to calibrate and validate a daily water balance model to estimate surface runoff losses across three rice-growing seasons. During the first two seasons, different model components were calibrated by comparing simulated and observed water depths. In the final season, the calibrated model was validated using direct runoff measurements obtained from weirs and flowmeters. Results showed strong agreement between model estimates and direct measurements of water depth and surface runoff. Linear regression models showed good fit, with coefficients of determination (R²) above 0.80 for water depth and 0.79 for runoff. A validated daily water balance model, combined with periodic monitoring of water depth, proved to be a reliable tool for estimating surface runoff during the rice-growing season. Total runoff—from irrigation, rainfall, and final drainage—represented between 7.5% and 18% of the total water input. This approach offers a practical tool for improving irrigation water management and understanding runoff-driven nutrient transport.