Farmers and policy makers pursue management practices that enhance water quality, increase landscape flood resiliency, and mitigate agriculture’s contribution to climate change, all while remaining economically viable. This study presents a holistic assessment of how two practices influence the supply of these ecosystem services—the use of an aerator prior to manure application in haylands, and the stacked use of manure injection, cover crops, and reduced tillage in corn silage production. Field data are contextualized by semi-structured interviews that identify influences on adoption. Causal loop diagrams then illustrate feedbacks from ecosystem services onto decision making. In our study, unseen nutrient pathways are the least understood, but potentially the most important in determining the impact of a practice on ecosystem services supply. Subsurface runoff accounted for 64% to 92% of measured hydrologic phosphorus export. Average soil surface greenhouse gas flux constituted 38% to 73% of all contributions to the equivalent CO2 footprint of practices, sometimes outweighing carbon sequestration. Farmers identified interest in better understanding unseen nutrient pathways, expressed intrinsic stewardship motivations, but highlighted financial considerations as dominating decision making. Our analysis elevates the importance of financial supports for conservation, and the need for comprehensive understandings of agroecosystem performance that include hard-to-measure pathways.