This groundwater-flow model archive contains all of the input and output files for an inset MODFLOW-NWT model extracted from the northern (Wisconsin) half of a published USGS steady-state regional model of the Upper Fox River Basin in the U.S. Upper Midwest. The construction and details of the published USGS steady-state model of the Upper Fox River Basin is outlined in the U.S. Geological Survey Scientific Investigations Report 2018-5038 (https://doi.org/10.3133/sir20185038). The regional model is archived in the data release at https://doi.org/10.5066/F76D5R5V. The extracted model was used to demonstrate an innovative new method for delinating fen distribution and discharge using the MODFLOW UZF package. The extracted model incorporates the Mukwonago River Basin, a 10-digit hydrologic unit code (HUC10) basin occupying 86.2 mi2 (223 km2) in southeastern Wisconsin. The extracted model was used to demonstrate how regional and local flow patterns can be enhanced by adding a version of the UZF file that automatically inserts “seepage drains” in cells where the water table is near the land surface (within the “undulation depth”). Details on the extracted model construction and calibration, including preparation of the “stripped-down” UZF file central to the proposed fen delineation method can be found in the supporting information of the journal article in Groundwater (https://doi.org/10.1111/gwat.12931). This USGS data release contains all of the input and output files for the simulations described in the journal article in Groundwater (https://doi.org/10.1111/gwat.12931).