Continuous use of agricultural chemicals and fertilizers, sporadic sewer overflow events and increase in urbanization have led to significant nutrients and pollutants loadings into the Arroyo Colorado River, located in South Texas. Priority nutrients requiring reduction include phosphorous and nitrogen whose continuous discharge has resulted in the impairment of the water quality in some of the river segments as well as a reduction in the amounts of Dissolved Oxygen present in the river. Consequently, the river’s potential to support aquatic life has been significantly reduced, thus highlighting the need for its restoration. To achieve restoration, a watershed protection plan was developed, which comprises of a number of mitigation measures including the installation of green infrastructure (GI) practices. For effective reduction of nutrient loadings however, there was a need to carry out a study on the effect of different combinations of GI practices under different future land use scenarios on the reduction of nitrogen and phosphorous to guide decision makers on the right infrastructure to be constructed while considering factors such as the existing drainage system, topography, land use, streamflow, and costs. Therefore, this study couples the Soil and Water Assessment Tool (SWAT) model with the System for Urban Stormwater Treatment and Analysis Integration (SUSTAIN) model to determine the effect of different combinations of GI practices on the reduction of phosphorous under changing land use conditions in three selected Arroyo Colorado sub-watersheds. Two land use maps from the USGS Forecasting Scenarios of land use (FORE-SCE) model scenarios for 2050 namely, A1B and B1 were analyzed in this study. Imperviousness increase is projected as 13.8% and 20.7% for each compared to the base case land use of 2018. Results from this study show that runoff, phosphorous and nitrogen amounts increase with the increase in imperviousness and infiltration-based GI practices will be more effective in the reduction of nutrients in the future under both A1B and B1 land use scenarios compared to treat and release systems and priorities need to be set by stakeholders regarding flow control and nutrient reduction. These results provide useful information to decision-makers, city planners, watershed managers, and other stakeholders involved in restoration efforts in the Arroyo Colorado basin.