In the current context of climate change, there is growing interest in the optimization of water management in irrigated areas, in semi-arid environments. The design of adequate adaptation and mitigation measures requires specific data at different scales of the water management hierarchy, up to basin level. In this work, the irrigation and drainage system of San Pedro de Castelflorite Irrigation Community (Huesca province, NE Spain), first set up as a flood irrigation system around 1970 and then modernized to sprinkler irrigation around 2008, was studied over two irrigation seasons. The land in this basin, with a surface of 11,450 ha, is affected by severe sodicity problems, which impedes cultivation in large areas. Most of the drainage water discharges into Clamor Vieja ravine, in which the quantity and quality of drainage, using water, salt, and nitrogen balances, were monitored. The water regime was found to be essentially regulated by irrigation. From the water balance, the consumed and the recoverable fractions were estimated at 76% and 23%, respectively, and the depleted beneficial fraction for the irrigated area at 73%. A predominance of salt dissolution processes over precipitation processes was found, with salt exports of approximately 2000 kg ha−1·year−1. The nitrogen exported by the drainage water was 7 kg N·ha−1·year−1. This value, remarkably lower than those reported for nearby basins in the central Ebro valley, can be attributed to the flooding of rice fields and to the low permeability of the soils present in this basin, which would hamper nitrate washing through the soil profile.