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Abstract Efficient management of nitrogen (N) and phosphorus (P) is imperative for sustainable agriculture, resource conservation, and reducing environmental pollution. Despite progress in on-farm practices and urban wastewater treatment in the Chesapeake Bay (CB) watershed, limited attention has been given to nutrient transport, use, and handling between farms and urban environments. This study uses the hierarchicalCAFE(Cropping system, Animal-crop system, Food system, and Ecosystem) framework to evaluate nutrient management performances within the watershed. We first develop a three-decade, county-level nutrient budget database (1985–2019), then analyze the spatiotemporal patterns of N and P budgets, as well as N and P use efficiencies, within the fourCAFEhierarchies. Our results indicate a sizable increase in potential N and P losses beyond crop fields (i.e. in the Animal-crop system, Food system, and Ecosystem), surpassing losses from cropland in over 90% of counties. To address these system-wide trade-offs, we estimate the nutrient resources in waste streams beyond croplands, which, if recovered and recycled, could theoretically offset mineral fertilizer inputs in over 60% of counties. Additionally, the growing imbalance in excess N versus P across systems, which increases the N:P ratio of potential losses, could pose an emerging risk to downstream aquatic ecosystems. By utilizing a systematic approach, our novel application of theCAFEframework reveals trade-offs and synergies in nutrient management outcomes that transcend agro-environmental and political boundaries, underscores disparities in N and P management, and helps to identify unique opportunities for enhancing holistic nutrient management across systems within the CB watershed.