Many conservation programs under the 2002 Farm Act address resource concerns such as water quality and aquatic communities in streams. Analyzing two such programs, simulated changes in agricultural practices decreased field-edge sediment losses by 25–31% in two geophysically distinct Minnesota watersheds. However, while in-stream sediment concentrations and lethal fisheries events decreased significantly in one watershed, there was no discernable improvement for the fisheries in the other, despite potentially spending over $100,000 annually in conservation payments. These results highlight the importance of performance-based conservation payments targeted to genuine resource concerns in watersheds and the value of integrated bioeconomic modeling of conservation programs.