This research contributes to the knowledge of the geothermal area of the Nevado del Ruiz Volcano (Colombia) by analyzing the secondary permeability and connectivity of fractures at microstructural and macrostructural level, comparing a zone affected by intense faulting with another one characterized by the same lithology, but with less influence of faulting and located further from the volcano. Fractured were identified and characterized in the field at outcrops with the window sampling method, and petrographic analysis was performed to confirm the mineralogy of rock samples collected. Simulations of groundwater flow and heat transfer in no fractured, low-fractured, and high-fractured are performed to quantify the impact of permeability observed in the field on the physical processes that involve geothermal resources circulation in a fractured reservoir. It was found that the faults do not directly influence the connection of fractures, but they influence the intensity of fractures. To analyze the influence of fractures on fluid flow, it is suggested to consider three main aspects: secondary permeability, connectivity, and fracture intensity. The location of hot springs can be associated with the macrostructural connectivity, to analyze the relation between secondary permeability and geothermal fluid circulation. The presented methodology is useful at the initial exploration stage in fractured geothermal reservoirs.