This dataset compiles measurements of permeability in crystalline rocks from two papers (Achtziger-Zupančič et al., 2017; Kuang & Jiao, 2014), providing a comprehensive database with 27,966 datapoints that covers different geological settings. We estimate effective fracture porosity and fracture density using permeability, aperture, and a roughness factor. The dataset is designed to support analyses of the relationship between hydraulic and petrophysical properties and depth, as well as the statistical distribution of these properties in low-permeability crystalline environments. Particular emphasis is placed on the strong variability and skewness of porosity and permeability values observed across datasets.