Groundwater storage, drainage, and interbasin water exchange are common hydrological processes but often difficult to quantify due to a lack of local observations. We present a study of three volcanic mountainous watersheds located in south‐central Chile (~36.9 ° S) in the Chillán volcanic complex (Chillán, Renegado, and Diguillín river basins). These are neighboring basins that are similar with respect to the metrics normally available for characterization everywhere (e.g., precipitation, temperature, and land cover). In a hydrological sense, similar (proportional) behavior would be expected if these catchments would be characterized with this general information. However, these watersheds show dissimilar behavior when analyzed in detail. The surface water balance does not fit for any of these watersheds individually; however, the water balance of the whole system can be explained by likely interbasin water exchanges. The Renegado river basin has an average annual runoff per unit of area on the order of 60–65% less than those of the Diguillín and Chillán rivers, which is contradictory to the hydrological similarity among the basins. To understand the main processes that control streamflow generation, two analyses were performed: (a) basin metrics (land cover, geologic, topographic, and climatological maps) and hydro‐meteorological data analyses and (b) a water balance model approach. The analyses contribute to a plausible explanation for the hydrogeological processes in the system. The soils, topography, and geology of the Chillán–Renegado–Diguillín system favor the infiltration and groundwater movements from the Renegado river basin, mainly to the neighboring Diguillín basin. The interbasin water exchanges affect hydrological similarity and explain the differences observed in the hydrological processes of these three apparently similar volcanic basins. The results highlight the complexity of hydrological processes in volcanic mountainous systems and suggest that a simple watershed classification approach based on widely available data is insufficient. Simple local analyses such as specific flow analysis with a review of the geology and morphology can contribute to a better understanding of the hydrology of volcanic mountainous areas.