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Submarine groundwater discharge is increasingly recognized as an important component of the oceanic geochemical budget, but knowledge of the distribution of this phenomenon is limited. To date, reports of meteoric inputs to marine sediments are typically limited to shallow shelf and coastal environments, whereas contributions of freshwater along deeper sections of tectonically active margins like the Chilean Margin have generally been attributed to silicate diagenesis, mineral dehydration, or methane hydrate dissociation. Here we report that substantial pore water freshening on the south Chilean Margin reflects deep and focused contributions of meteorically modified geothermal groundwater, which has infiltrated marine sediments through regional fault systems. Geochemical fingerprinting of pore water data from Site J1003, recovered during D/V JOIDES Resolution Expedition 379T, highlights mixing between this fresh groundwater endmember and seawater, and provides the first constraints on the depth of geothermal groundwater reservoirs in the Aysén region of Patagonia. Collectively, our results identify an unappreciated locus of deep submarine groundwater and geothermal discharge along active margins, with potential implications for coastal biogeochemical processes and tectonic instability.