In this paper we present a Strategic Environmental Assessment (SEA) case-study applied to a Rural Development Program (RDP), which allocates resources to support agri-environmental schemes to pay farmers for the provision of environmental services. In particular, the paper examines the use of spatially explicit assessment methods. The results show that the spatial distribution of certain key environmental measures is not always the best-performing one in environmental terms, based on a series of spatially explicit environmental indexes. Spatial analysis thus represents a useful tool for providing input to decision-makers, especially when dealing with complex instruments such as RDP that entail consideration of a variety of objectives, stakeholders, beneficiaries, and environmental aspects.