The Environmental Quality Incentives Program and other voluntary Federal conservation programs follow a similar approach for enrollment. Consistent with the legislation, agency personnel identify eligibility criteria, suitable conservation practices, and a process to score, rank, and select applications for funding. Our research outlines a formal multiple criteria decision analysis system that is broadly applicable to current Federal conservation programs to score, rank, and enroll applications, and distribute program funds. Then, we apply the decision system to Indiana’s EQIP program using data from 2005. The incorporation of GLEAMS model improved our estimates of water quality impacts by reintroducing the spatial heterogeneity.