Spatially targeted interventions improve the effectiveness of environmental policy, but are challenged by implementation constraints and coordination among governments. Spatial targeting research rarely acknowledges the diversity of actors navigating complicated institutional dynamics to deploy environmental policy instruments. We mapped 35 nutrient reduction interventions by federal, state, county, and municipal governments and interviewed 15 policymakers and agency staff in Wisconsin’s Yahara Watershed, USA to understand how multilevel governance impacts spatial targeting and implementation of water quality policy. Our Geographic Information System database showed that county governments implemented the most policies, while the state promulgated the most rules, with uneven application of policy interventions across the landscape. Spatial targeting differed between agricultural and non-agricultural policies and by type of tool (land acquisition, direct management, incentive, and regulation). We found a negative correlation between areas of policy intervention and phosphorus load across government levels (p< 0.001), with the strongest negative correlations by implementing agency level. Interviews revealed that for public organizations, spatial targeting is in tension with program and funding constraints and imperfect information about soil and land use practices. In order to target the highest phosphorus yielding subwatersheds, governments will need to alter the spatial location of their efforts.