Draining mine tunnels contribute contaminants to groundwater and surface water, but remediation strategies may be hindered as hydrogeologic characterization and modeling of these heterogeneous features generally relies on sparse data sets. The Captain Jack mine site in Colorado, USA, presents a unique data set allowing for temporal evaluation of groundwater connectivity in the vicinity of an abandoned mine, where a hydraulic bulkhead is impounding water within the mine workings. This study applied statistical analysis of system pressure responses to bulkheading and used an analytic-element modeling approach to characterize heterogeneity and groundwater flow. Groundwater-level elevation data collected over a period of 4 years, both prior to and after bulkheading, indicate that the mine workings act as a sink to the local groundwater system. Despite groundwater flow being generally oriented towards the mine workings, there are also large vertical and horizontal hydraulic gradients which persist through time. Although the groundwater system is highly compartmentalized, statistical analysis using Kendall’s Tau indicates correlations between hydraulic head changes in the mine workings and several wells completed in crystalline bedrock, indicating the influence of fracture flow. An analytic-element model was parameterized to account for uncertainty in hydraulic conductivity, recharge, and discharge. Model results reproduced the range of observed hydraulic heads in the mine workings and adjacent igneous dikes but failed to closely simulate hydraulic heads in several wells located distal from the mine workings in granitic bedrock. The modeling approach shows potential promise, however, for conducting preliminary modeling to guide data collection at other similar mine sites.