This report describes the regional hydrogeology and groundwater resources of Columbia County, Wisconsin, and documents a regional groundwater flow model developed for the county. Regional hydrostratigraphic units include the unlithified aquifer, the upper bedrock aquifer, and the Elk Mound aquifer. The unlithified aquifer consists of deposits that range in composition from sand and gravel outwash and stream deposits to silty, sandy till. This aquifer is less than 25 ft thick in much of eastern Columbia County, but consists of permeable sand and gravel extending to over 250 ft in depth in the Wisconsin River valley bottom. The upper bedrock aquifer consists of Ordovician and upper Cambrian sedimentary formations, including sandstone, siltstone and dolomitic strata. The upper bedrock aquifer underlies the unlithified aquifer in eastern portions of the County, but is absent to the west, where these formations are largely eroded. The contact between the Tunnel City Group and Wonewoc Formation (Top of Elk Mound Group) forms the base of the upper bedrock aquifer. Bedding plane fractures are common to this aquifer, although only a portion of the observed fractures appear to be hydraulically active. The upper bedrock aquifer is a significant source of groundwater at a regional scale. Measurements of hydraulic head showed a difference of several feet across the bottom of this aquifer to the underlying Wonewoc sandstone, indicating that the basal facies of the Tunnel City Group functions as an aquitard separating the upper bedrock aquifer from the Elk Mound aquifer. Conditions vary considerably within this aquifer, depending on the local lithostratigraphy. For example, where present, the St. Lawrence Fm. and fine-grained intervals of the Tunnel City Group may be locally-extensive aquitards. The Elk Mound aquifer consists of Cambrian sandstone of the Wonewoc, Eau Claire, and Mount Simon Formations. It is thin to absent in several locations but ranges up to 600 ft in thickness over much of southern Columbia County. The variation in thickness is due in large part to the irregular topography of the underlying Precambrian crystalline rock, which generally serves as the base of the groundwater system. In neighboring counties, a fine-grained facies within the Eau Claire Fm. acts as a regionally extensive aquitard, referred to as the Eau Claire aquitard. Much of the data collected and compiled for this study suggest that shale or dolomite within the Eau Claire Fm., which is the equivalent of the Eau Claire aquitard, occurs only within southwestern Columbia County. There is little to no evidence of the Eau Claire aquitard over most of the county. Where the dolomite and shale are absent, the Elk Mound aquifer is relatively homogenous and does not include a mappable aquitard. A three-dimensional steady-state flow model presented here represents long-term, average conditions in the regional groundwater system since about 1970. The model was constructed with the U.S. Geological Survey’s MODFLOW-NWT code; it has six layers with a uniform grid of 300 ft x 300 ft cells. Layers 1 and 2 simulate the unlithified aquifer and layer 3 represents the upper bedrock aquifer. The Elk Mound aquifer is simulated by layers 4, 5 and 6, representing the Wonewoc, Eau Claire, and Mount Simon Formations, respectively. The model extends beyond the boundaries of Columbia County to ensure that hydrologic conditions simulated within the County are consistent with regional conditions. Recharge to the groundwater flow model is based on results from a GIS-based soil-water-balance model. Recharge was simulated with the unsaturated zone flow (UZF) package in MODFLOW. This approach is particularly useful for quantifying groundwater discharge to riparian wetlands because UZF tracks recharge that would lead to the simulated water table exceeding the land surface (represented by the top of model layer 1) and reroutes it to nearby stream segments. The model includes pumping from 256 wells, and 178 of these are located within Columbia County. Pumping totaled about 28 million gallons per day (mgd) on average since 1970, with 7.2 mgd of the withdrawal from within the County. Model calibration was performed with the PEST parameter estimation code. Calibration targets included approximately 3,900 head measurements and 91 stream flow measurements. Four vertical-head differences across hydrogeologic units, calculated from data collected during packer testing in wells in Columbia County, were also used in model calibration. Results from the calibrated model provide a groundwater balance for the region. About 83 percent of groundwater originates as recharge to the water table, 12 percent comes from leakage from streams, and about 5 percent of the groundwater flows into the model domain from surrounding areas. About 95 percent of the simulated groundwater discharges to steams and other surface water features, about 3 percent flows across model boundaries to surrounding areas of the groundwater system, and pumping accounts for 2 percent of discharge. Simulated flow paths are relatively local, from recharge in upland areas to discharge in nearby streams and wetlands. The model has many potential applications, including simulation of the effects of existing or proposed high-capacity wells, estimating the zone of contribution for these wells, and understanding relationships between surface water and groundwater. Future refinements to the model, such as incorporating new information about the extent and hydraulic characteristics of the Tunnel City Group, will improve its utility in understanding advective flow between the upper bedrock and Elk Mound aquifers. If seasonal or annual variations in the groundwater system are of interest, this steady-state model could be brought into a transient mode.