Political agendas worldwide include increased production of biofuel, which multiplies the trade-offs among conflicting objectives, including food and fodder production, water quantity, water quality, biodiversity, and ecosystem services. Quantification of trade-offs among objectives in bioenergy crop production is most frequently accomplished by a comparison of a limited number of plausible scenarios. Here we analyze biophysical trade-offs among bioenergy crop production based on rape seed, food crop production, water quantity, and water quality in the Parthe catchment in Central Germany. Based on an integrated river basin model (SWAT) and a multi-objective genetic algorithm (NSGA-II), we estimated Pareto optimal frontiers among multiple objectives. Results indicate that the same level of bioenergy crop production can be achieved at different costs with respect to the other objectives. Intermediate rapeseed production does not lead to strong trade-offs with water quality and low flow if a reduction of food and fodder production can be accepted. Compared to solutions focused on maximizing food and fodder yield, solutions with intermediate rapeseed production even improve with respect to water quality and low flow. If rapeseed production is further increased, negative effects on low flow prevail. The major achievement of the optimization approach is the quantification of the functional trade-offs for the feasible range of all objectives. The application of the approach provides the results of what is in effect an infinite number of scenarios. We offer a general methodology that may be used to support recommendations for the best way to achieve certain goals, and to compare the optimal outcomes given different policy preferences. In addition, visualization options of the resulting non-dominated solutions are discussed.