Disclosed are a system and method configured for detecting cosmic ray muon (CRM) flux along a variety of trajectories through a subterranean test region, collecting the muon detection data, and processing the data to form a three-dimensional density distribution image corresponding to the test region. In at least one embodiment, the system may be used for identifying concentrations of higher (or lower) density mineral deposits or other geological structures or formations well below the earth's (or ocean floor) surface. The system may be utilized for imaging geological materials and structures of higher and/or lower density in a test region having a depth of several kilometers or more.