There is an abundant supply of corn stover in the United States that remains after grain is harvested which could be used to produce cellulosic biofuels mandated by the current Renewable Fuel Standard (RFS). This research integrates the Soil Water Assessment Tool (SWAT) watershed model and the DayCent biogeochemical model to investigate water quality and soil greenhouse gas flux that results when corn stover is collected at two different rates from corn-soybean and continuous corn crop rotations with and without tillage. Multiobjective watershed-scale optimizations are performed for individual pollutant-cost minimization criteria based on the economic cost of each cropping practice and (individually) the effect on nitrate, total phosphorus, sediment, or global warming potential. We compare these results with a purely economic optimization that maximizes stover production at the lowest cost without taking environmental impacts into account. We illustrate trade-offs between cost and different environmental performance criteria, assuming that nutrients contained in any stover collected must be replaced. The key finding is that stover collection using the practices modeled results in increased contributions to atmospheric greenhouse gases while reducing nitrate and total phosphorus loading to the watershed relative to the status quo without stover collection. Stover collection increases sediment loading to waterways relative to when no stover is removed for each crop rotation-tillage practice combination considered; no-till in combination with stover collection reduced sediment loading below baseline conditions without stover collection. Our results suggest that additional information is needed about (i) the level of nutrient replacement required to maintain grain yields and (ii) cost-effective management practices capable of reducing soil erosion when crop residues are removed in order to avoid contributions to climate change and water quality impairments as a result of using corn stover to satisfy the RFS.