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The inherent variability in corn stover productivity due to variations in soils and crop management practices might contribute to a variation in corn stover-based bioethanol sustainability. This study was carried out to examine how changes in soil types and crop management options would affect corn stover yield (CSY) and the sustainability of the stover-based ethanol production in the Delta region of Mississippi. Based on potential acreage and geographical representation, three locations were selected. Using CERES-Maize model, stover yields were simulated for several scenarios of soils and crop management options. Based on 'net energy value (NEV)' computed from CSYs, a sustainability indicator for stover-based bioethanol production was established. The effects of soils and crop management options on CSY and NEV were determined using ANOVA tests and regression analyses. Both CSY and NEV were significantly different across sandy loam, silt loam, and silty clay loam soils and also across high-, mid-, and low-yielding cultivars. With an increase in irrigation level, both CSY and NEV increased initially and decreased after reaching a peak. A third-degree polynomial relationship was found between planting date and CSY and NEV each. By moving from the lowest to the highest production scenario, values of CSY and NEV could be increased by 86 to 553%, depending on location and weather condition. The effects of variations in soils and crop management options on NEV were the same as on CSY. The NEV was positive for all scenarios, indicating that corn stover-based ethanol production system in the Delta region is sustainable.