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Underground monument preservation is tightly linked to geological risk. The geological risk management of underground structures typically relies on a preliminary site investigation phase. Engineering geological mapping—as a key site investigation element—is largely based on manual in situ work, often in harsh and dangerous environments. However, although new technologies can, in many cases, decrease the on-field time as well as eliminate inaccessibility issues, the example presented in this study demonstrates a special challenge that had to be addressed. The ancient underground marble quarries of Paros Island in Greece constitute a gallery complex of a total length of 7 km and only two portals, resulting in total darkness throughout almost the full length of the unsurveyed galleries. As such, the entire survey and engineering geological mapping solely relied on a virtual reality application that was developed based on a digital replica of the quarries using laser scanning. The study identifies several critical locations with potentially unstable geologic structures and computes their geometrical properties. Further numerical analyses based on data extracted directly from the digital replica of the rock mass led to the definition of appropriate risk mitigation measures along the underground marble quarries.