The harvest of corn stover or herbaceous crops as feedstocks for bioenergy purposes has been shown to have significant benefits from energy and climate change perspectives. There is a potential, however, to adversely impact water and soil quality, especially in Midwestern states where the biomass feedstock production would predominantly occur. The overall goal of this research is to provide a thorough and mechanistic understanding of the relationship between stover and/or herbaceous crop production management practices and resulting range of impacts on soil and water quality, with a focus on Eastern Iowa. The production of these bioenergy crops is compared to corn and corn-soybean rotations on eight different soils representative of the region. The APEX model, which predicts crop, water, nutrient, carbon and soil flows within an integrated agricultural and hydrological system, provides a means to quantify sustainability metrics and is used to generate sufficient data to provide a greater understanding of the particular variables that affect water and soil quality than previously possible. The sustainability metrics include total nutrient emissions to ground and surface water, total soil losses due to wind and water erosion, and cumulative soil carbon losses, all normalized to both acreage and the energy value of the potential biofuel production. As expected, the results clearly show the superiority of switchgrass from a soil and water quality perspective. They also show, however, that compared to corn-soybean rotations with conventional tillage, soil and water quality degradation can be reduced at the same time stover is collected under certain soil types and no-till agricultural practices. An analysis of variance identifies the most critical variables correlated to each of the sustainability metrics, thereby helping to identify the conditions that should be given the highest priority for sustainable bioenergy crop production.