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Over the past century, mesquite trees (Prosopis spp.) have exhibited substantial increase in abundance throughout areas in the American Southwest that were once dominated by desert grassland. To assess hydrological consequences of mesquite encroachment, the Soil and Water Assessment Tool (SWAT) was applied to simulate progressive mesquite encroachments in the upper San Pedro watershed (U.S./Mexico). The simulated average annual basin evapotranspiration (ET) increases with mesquite encroachment, leading to the decrease of annual water yield and percolation by 9.8% and 9.7%, respectively. Substantial increase of ET (up to 19.19 mm) and decrease of percolation, and surface runoff (to -12.90 and -3.20 mm, respectively) were observed in the southeast, middle-west, and northern subwatersheds of the basin and the most significant decrease of surface runoff (around -35.8%) was simulated during the wet period. In addition, a non-linear hydrological response relative to mesquite encroachment was observed, i.e. hydrological processes changed markedly until a certain amount (approximately 40%) of grassland was removed, indicating that the strongest increase of ET occurred in the earliest stages of encroachment. Consequently, changes in vegetation physiognomy, such as mesquite encroachment, have broad implications for landuse management especially in regard to reliable water supplies in arid and semi-arid environments. Published by Elsevier Ltd.