AbstractSpatial and temporal distribution of nitrate, phosphate, and salinity of complex soil and water system is essential for land and water resources management. In this study, by aggregating a flow [SWAP (Soil-Water-Air-Plant)] and a transport [ANIMO (Agricultural Nitrogen Model)] model, the regional distributions of salinity, nitrate, and phosphate for an irrigation district, west of Iran, were simulated. Precise sensitivity analysis, calibration, and validation were performed based on the observed values. The results revealed that the soil salinity did not have considerable change with depth, but nitrate and phosphate decreased by about 42% and 92%, respectively. The effects of irrigation, fertilization, and seasonal weather changes on concentration of concerned parameters was also simulated well in time series. The mass balance results indicated that more salt had outflows from and more nitrate and phosphate remained in the soil, which could be a sign of soil deterioration. This spatial-temporal distributed model of unsaturated zone could be used for evaluation of long-term irrigation management scenarios while considering soil and water quantity and quality indicators.