This U.S. Geological Survey (USGS) data release contains model scenario input and output files and nine hydrology and water-quality models developed using the Soil and Water Assessment Tool (SWAT). The models represent nine watersheds in eastern New York that drain to Lake Erie or the Niagara River and were created, calibrated, and validated for hydrology, sediment, and nutrients as baseline scenarios. Twenty-six additional scenarios were created to explore the effects of agricultural and urban best management practices, point source discharges, and green infrastructure on the water quality of tributaries to Lake Erie/Niagara River. Model documentation and scenario development are described in Merriman and others (2024).