A comprehensive worldwide permeability data set has been compiled consisting of 29,000 in situ permeabilities from 221 publications and reports and delineating the permeability distribution in crystalline rocks into depths of 2000 meters below ground surface (mbgs). We analyze the influence of technical factors (measurement method, scale effects, preferential sampling, and hydraulic anisotropy) and geological factors (lithology, current stress regime, current seismotectonic activity, and long‐term tectonogeological history) on the permeability distribution with depth, by using regression analysis and k‐means clustering. The influence of preferential sampling and hydraulic anisotropy are negligible. A scale dependency is observed based on calculated rock test volumes equaling 0.6 orders of magnitude of permeability change per order of magnitude of rock volume tested. Based on the entire data set, permeability decreases as log(k) = −1.5 × log(z) − 16.3 with permeability k (m2) and positively increasing depth z (km), and depth is the main factor driving the permeability distribution. The permeability variance is about 2 orders of magnitude at all depths, presumably representing permeability variations around brittle fault zones. Permeability and specific yield/storage exhibit similar depth trends. While in the upper 200 mbgs fracture flow varies between confined and unconfined, we observe confined fracture and matrix flow below about 600 mbgs depth. The most important geological factors are current seismotectonic activity (determined by peak ground acceleration) and long‐term tectonogeological history (determined by geological province). The impact of lithology is less important. Based on the regression coefficients derived for all the geological key factors, permeability ranges of crystalline rocks at site scale can be predicted. First tests with independent data sets are promising.