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Cellulosic and agricultural bio-energy crops can, under careful management, be harvested as feedstock for bio-fuels production and provide environmental benefits. However, it is required to quantify their relative advantages in feedstock production and water quality. The primary objective of this research was to evaluate potential feedstock yield and water quality benefit scenarios of bio-energy crops: Miscanthus (Miscanthus-giganteus), Switchgrass (Panicum virgatum), Johnsongrass (Sorghum halepense), Alfalfa (Medicago sativa L.), Soybean {Glycine max (L.) Merr.}, and Corn (Zea mays) in the Upper Pearl River watershed (UPRW), Mississippi using a Soil and Water Assessment Tool (SWAT).