Grain-crop biomass and perennial grass biomass are of particular interest for their use in bioenergy production systems. Nutrient needs, particularly nitrogen and phosphorus, change with varying cropping systems, harvest systems, and rates of fertilizer application. Furthermore, manure generated from livestock production can be a viable nutrient source for cropping systems, reducing the need for commercial fertilizers. The primary focus of this study was to investigate nutrient loss, primarily nitrate-nitrogen loss, in subsurface drainage water under a variety of cropping, nutrient management, and harvest scenarios. Overall crop yields and biomass production were also evaluated.</p