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. Although the Nevado del Ruiz Volcano (NRV) area has had geothermal exploration studies for power generation since 1968, there is still no exploitation of its geothermal resources. The NRV geothermal reservoir is characterized by a low primary permeability and the presence of several geological faults crossing a tectonically active and complex region. The analysis was performed 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. Fractures were characterized at outcrops with the window sampling method, and petrographic analysis was performed to confirm the mineralogy of samples collected. At the microstructural scale it was found that faulting does not necessarily influence the interconnectivity of fractures, but it does influence their intensity, quantity, and strike. To analyze the influence of fractures on groundwater flow, it is suggested to consider three main aspects: secondary permeability, connectivity, and fracture intensity. The lithology of major geothermal interest in the NVR area (Pes) presented greater connectivity and fracture intensity, which, combined with the high foliation observed in field, increase its effective permeability. The secondary permeability of different lithologies in the NRV area ranged between 1.15 × 10–6 and 10.32 × 10–7 m2. Most of the hot springs were in areas of high macrostructural connectivity, supporting the idea that groundwater flow is dominated by the secondary permeability of rocks. Estimation of the secondary permeability and identification of areas of high fracturing and connectivity, contributes to the understanding of the NRV geothermal area, which is a key aspect when drilling for successful well production. The methodology presented is useful in the initial exploration phase in fractured geothermal reservoirs. © The Author(s) 2024.