This study uses the hierarchical CAFE (Cropping system, Animal-crop system, Food system, and Ecosystem) framework to evaluate nutrient management performances within the Chesapeake Bay watershed. This dataset contains a three-decade, county-level nutrient budget (1985–2019), which can be used to analyze the spatiotemporal patterns of N and P budgets, as well as N and P use efficiencies, within the four CAFE hierarchies. This dataset is associated with the following publication: Zou, T., E. Davidson, R. Sabo, G. MacDonald, and X. Zhang. Disparities in nitrogen and phosphorus management across time and space: a case study of the Chesapeake Bay using the CAFE framework. Environmental Research Letters. IOP Publishing LIMITED, Bristol, UK, Volume 19: 110016, (2024).