For over three decades, Chesapeake Bay (USA) has been the focal point of a coordinated restoration strategy implemented through a partnership of governmental and nongovernmental entities, which has been a classical model for coastal restoration worldwide. This synthesis aims to provide resource managers and estuarine scientists with a clearer perspective of the magnitude of changes in water quality within the Bay watershed, including nitrogen (N), phosphorus (P), and sediment for the River Input Monitoring (RIM) watershed and the unmonitored below-RIM watershed. The flow-normalized N load from the RIM watershed has declined in the period of 1985–2017, but P and sediment loads have lacked progress. Reductions of riverine N are largely driven by reductions of point sources and atmospheric deposition. Future reductions will require significant progress in managing agricultural nonpoint sources. The below-RIM watershed, which comprises a disproportionately high fraction of inputs to the Bay, has shown long-term declines in major sources, including point sources (N and P), atmospheric deposition (N), manure (N and P) and fertilizer (P), based on a combination of monitoring and modeling assessments. To date, the Bay cleanup efforts have achieved some progress toward reducing nutrients from the watershed, which have resulted in improving water quality in the estuary. However, further reductions are critical to achieve the Chesapeake Bay Total Maximum Daily Load goals, and emerging challenges due to Conowingo Reservoir, legacy nutrients, climate change, and population growth should be considered. Continued monitoring, modeling, and assessment are critically important for informing the restoration of this complex ecosystem.