High-altitude peatlands in the Andes, i.e., bofedales, play an essential role in alpine ecosystems, regulating the local water balance and supporting biodiversity. This is particularly true in semiarid Chile, where bofedales develop near the altitudinal and hydrological limits of plant life. The subterranean geometry and stratigraphy of one peatland was characterized in north-central Chile using Electrical Resistivity Tomography (ERT), Ground Penetrating Radar (GPR) and core extraction. Two sounding locations, two transversal and one longitudinal profile allowed a 3D interpretation of the bofedal’s internal structure. A conceptual model of the current bofedal system is proposed. Geophysical results combined with porosity measurements were used to estimate the bofedal water storage capacity. Using hydrological data at the watershed scale, implications regarding the hydrological role of bofedales in the semiarid Andes were then briefly assessed. At the catchment scale, bofedal water storage capacity, evapotranspiration losses and annual streamflow are on the same order of magnitude. High-altitude peatlands are therefore storing a significant amount of water and their impact on basin hydrology should be investigated further.