Between 25% and 85% of water inputs to rice fields are lost by seepage and percolation. These losses can be reused downstream and do not necessarily lead to true water depletion at the irrigation system level. Because of this potential for reuse, the general efficiency of water use can increase with increasing spatial scale. To test this hypothesis, a multi-scale water accounting study was undertaken in District I of the rice-based Upper Pampanga River Integrated Irrigation System (UPRIIS) in the Philippines. Daily measurements of all surface water inflows and outflows, rainfall, evapotranspiration, and amounts of water internally reused through check dams and shallow pumping were summed into seasonal totals for 10 spatial scale units ranging from 1500 ha to 18,000 ha. The amount of net surface water input (rainfall plus irrigation) per unit area decreased and the process fraction, depleted fraction, water productivity, and amount of water reuse increased with increasing spatial scale. In total, 57% of all available surface water was reused by check dams and 17% by pumping. The amount of water pumped from the groundwater was 30% of the amount of percolation from rice fields. Because of the reuse of water, the water performance indicators at the district level were quite high: the depleted fraction of available water was 71%, the process fraction of depleted water was 80% (close to the 75% area covered by rice), water productivity with respect to available water was 0.45 kg grain m−3 water, and water productivity with respect to evapotranspiration was 0.8 kg grain m−3 water. Water use in the district can be reduced by cutting down the 49 × 106 m3 uncommitted outflows. The depleted fraction of available water can be increased to 80% or more by a combination of adopting alternate wetting and drying (AWD) and increased pumping to capture percolating water. Water productivity with respect to available water can be increased to 0.83 kg grain m−3 water b combination of reduced land preparation time, adoption of AWD, and increased fertilizer N use to increase yields.