The Tolhuaca hydrothermal system is one of the few attested geothermal resources in Chile. While recent investigations provided some insights into the depth and temperature of the geothermal reservoirs and the chemical and mineralogical evolution of the hydrothermal system, little is still known about the CO2 degassing of the system and the local and shallow control of fluid pathways. Here, we document the soil CO2 degassing and soil temperature distributions in the southern part of the Tolhuaca hydrothermal system and at one of its northern fumaroles, and provide a first estimate of its total CO2 release. The surveyed area is responsible for a total CO2 emission of up to 30 t d−1. Hydrothermal CO2 emissions (~ 4–27 t d−1) are mostly restricted to the thermal manifestations or generally distributed along NNW trending lineaments, sharing the same orientation as the volcanic vents and thermal springs and fumaroles. Hydrothermal CO2 fluxes, fumaroles and thermal springs are generally encountered in topographic lows, in close vicinity of streams and often in clay-rich pyroclastic units, highlighting a relation between landscape evolution and the activity of the hydrothermal system. We suggest that glacial unloading and incision of the stream inside the clay-rich units have likely enhanced locally the permeability, creating a preferential pathway for the migration of deeper fluid to the surface. As several hydrothermal systems in the Andes are found on the flank of volcanoes hosting glaciers, we propose that they could have had a similar development to that of the Tolhuaca hydrothermal system.