A Groundwater Nitrate Decision Support Tool (GW-NDST) for wells in Wisconsin was developed to assist resource managers with assessing how legacy and possible future nitrate leaching rates, combined with groundwater lag times and potential denitrification, influence nitrate concentrations in wells (Juckem et al. 2024). The GW-NDST relies on several support models, including machine-learning models that require numerous GIS input files. This data release contains all GIS files required to run the GW-NDST and its machine-learning support models. The GIS files are packaged into three ZIP files (WI_County.zip, WT-ML.zip, and WI_Buff1km.zip) which are contained in this data release. Before running the GW-NDST, these ZIP files need to be downloaded and unzipped inside the "data_in/GIS/" subdirectory of the GW-NDST. The GW-NDST can be downloaded from the official software release on GitLab (https://doi.org/10.5066/P13ETB4Q). Further instructions for running the GW-NDST, and for acquiring requisite files, can be found in the software's readme file.