This is the geospatial and hydroclimate input data used to develop data-driven Machine Learning (ML) models as well as model estimated water quality based risk metrics and watershed health composite measure in three river basins in the Midwest. Model outputs that are used to construct the figures in the paper are displayed in the Excel file with the definitions of the data reported in each datasheet. The directory to the GIS data that were used to construct the inputs and spatially distributed risk metrics at the HUC-10 level is listed here and in the Scientific Data Management Plan. Portions of this dataset are inaccessible because: Large size GIS database. They can be accessed through the following means: C:\Users\MHantush\OneDrive - Environmental Protection Agency (EPA)\ScienceHUB\WH ML Modeling. Format: Generic GIS database.