The assessment of the geothermal resources available in a specific area requires a detailed knowledge of the thermal and hydraulic properties of host rock formations. These properties were quantified with rock samples mainly collected at the intersection between Nereidas, Cueva-Pirineos, and La Tosca-El Descanso faults, to the West of the Nevado del Ruiz volcano (Colombia), to improve the characterization of this volcanic geothermal system. The geological formations analyzed in this study are the Cajamarca Complex, PRE-Ruiz lava flows, Andesites unit, and volcanic member of the Quebradagrande Complex. A 3D geological conceptual model for the study area and a geological cross-section are presented. 113 laboratory measurements allowed to quantify thermal conductivity (TC) and diffusivity (TD), heat capacity (HC), porosity, and permeability of the rock samples collected. The Cajamarca Complex is the lithology with the highest TC (2.9 W m−1 K−1), but with the lowest primary permeability (0.038mD) and porosity (3.4%). Regarding extrusive igneous rocks, the Andesites unit present significative porosity (10.7%), and the PRE-Ruiz lava flows show a low TC (1.5 W m−1 K−1). The results of 6 petrographic analyses of thin sections of the PRE-Ruiz lava flows and Cajamarca Complex helped to justify the values of their thermal properties. Quartz-filled veinlets and garnet are identified in the volcanic member of the Quebradagrande Complex. Both minerals indicate that fluids might have circulated at high temperature. It is the first time that garnet is identified in rock samples of this region; since it can be the result of high temperature hydrothermal alteration mineral, its origin must be confirmed, and its identification provides new insights about the geothermal resources in the area. The conceptual model, the thin section results, and the quantification of rock properties are relevant public data for future geothermal development. All data reported in this manuscript are disclosed as supplementary material, providing a significant scientific contribution in the form of an open dataset that can be used as a basis for future hydrothermal modelling of the Nevado del Ruiz geothermal system, where is the most advanced geothermal development project in Colombia, and other similar geothermal systems.