Vertical flow in open boreholes is common in fractured rock because the borehole will hydraulically cross-connect the active fractures intersecting the hole. This study uses an equivalent porous medium (EPM) numerical model to examine the effect of an open borehole on the flow system and the vulnerabilities surrounding HBP5, a single 85 m deep open borehole cored through the multiple members of the Silurian-aged dolostone aquifer. Using high-resolution datasets is imperative to develop hydraulically-informed, process-based site conceptual models (SCMs) that can be used to build numerical models to give insight into the changes in groundwater flow behavior caused by the existence of HBP5. A suite of discrete fracture network and matrix (DFN-M) field measurement methods tailored for bedrock boreholes were used to characterize the subsurface under open and sealed-hole conditions (e.g., core inspection of lithology, ATV log, TVP log, video log, flow logging, and straddle packer head profile) to create a robust, hydrogeologic SCM. The numerical model developed from the SCM was shown to reasonably match the hydraulic data collected in the open hole and other wells throughout the study area (i.e., the flow log and the head profile in the open hole, and the heads from nearby wells). The hydraulic cross-connection was then simulated under various scenarios. The results demonstrate how varying open hole conditions open borehole disturb the natural flow conditions leading to erroneous estimation of hydraulic properties and misleading interpretations of data used for aquifer management decisions. Flow in bedrock aquifers is controlled by discrete fractures that were quantified using the multiple high-resolution methods, allowing the identification of hydraulically significant features intersecting the borehole that supported the interpretation of the system conditions and demonstrates how to work between DFN and EPM frameworks. Hydraulic cross-connection caused by open boreholes is very important when considering aquifer and well vulnerability, especially when contaminated sites exist, because these open holes create preferential pathways for re-directing shallow water that moves more readily into the deeper aquifer, increasing the vulnerability of the deeper aquifer.