Nonpoint source (NPS) pollutants such as phosphorus, nitrogen, sediment, and pesticides are the foremost sources of water contamination in many of the water bodies in the Midwestern agricultural watersheds. This problem is expected to increase in the future with the increasing demand to provide corn as grain or stover for biofuel production. Best management practices (BMPs) have been proven to effectively reduce the NPS pollutant loads from agricultural areas. However, in a watershed with multiple farms and multiple BMPs feasible for implementation, it becomes a daunting task to choose a right combination of BMPs that provide maximum pollution reduction for least implementation costs. Multi-objective algorithms capable of searching from a large number of solutions are required to meet the given watershed management objectives. Genetic algorithms have been the most popular optimization algorithms for the BMP selection and placement. However, previous BMP optimization models did not study pesticide which is very commonly used in corn areas. Also, with corn stover being projected as a viable alternative for biofuel production there might be unintended consequences of the reduced residue in the corn fields on water quality. Therefore, there is a need to study the impact of different levels of residue management in combination with other BMPs at a watershed scale. In this research the following BMPs were selected for placement in the watershed: (a) residue management, (b) filter strips, (c) parallel terraces, (d) contour farming, and (e) tillage. We present a novel method of combing different NPS pollutants into a single objective function, which, along with the net costs, were used as the two objective functions during optimization. In this study we used BMP tool, a database that contains the pollution reduction and cost information of different BMPs under consideration which provides pollutant loads during optimization. The BMP optimization was performed using a NSGA-II based search method. The model was tested for the selection and placement of BMPs in Wildcat Creek Watershed, a corn dominated watershed located in northcentral Indiana, to reduce nitrogen, phosphorus, sediment, and pesticide losses from the watershed. The Pareto optimal fronts (plotted as spider plots) generated between the optimized objective functions can be used to make management decisions to achieve desired water quality goals with minimum BMP implementation and maintenance cost for the watershed. Also these solutions were geographically mapped to show the locations where various BMPs should be implemented. The solutions with larger pollution reduction consisted of buffer filter strips that lead to larger pollution reduction with greater costs compared to other alternatives.