This report describes the setup, calibration, validation, and scenario analysis using the SWAT model to simulate the flow and water quality of the Arroyo Colorado watershed. The basin was subdivided into 17 subbasins-six in Segment 2201 and eleven in Segment 2202. The basin was characterized by a set of 475 hydrologic response units (HRUs) that are unique combinations of land cover, soil, and slope. For flow, 8 hydrologic process-related parameters were calibrated. A total of 26 process-related parameters were calibrated for water quality. Eleven years (1999-2009) of precipitation, air temperature, streamflow, and water-quality data were used for model calibration and validation. We used precipitation data from three stations; air temperature data from two stations; and streamflow data from two stations. Most of the water quality data used for model calibration and testing came from the station near Harlingen, Texas. Some water quality data available near Mercedes, Texas were also used in the study. Status of water quality in the river at present and for years 2015 and 2025 were projected using estimated land cover maps. Suggested solutions to bring dissolved oxygen in compliance for the stream were also discussed.