In recent decades, global dissolved oxygen (DO) measurements have registered a decrease of ∼1%–2% in oxygen content, raising concerns regarding the negative impacts of ocean deoxygenation on marine life and the greenhouse gas cycle. By combining in situ data from 2016 to 2022, satellite remote sensing, and outputs from a physical-biogeochemical model, we revealed the deoxygenation process in the Patagonian fjords for the first time. Deoxygenation was associated with the advection of equatorial subsurface water (ESSW) mass into the northern region of Patagonia. An analysis of the circulation regime using the Mercator-Ocean global high-resolution model confirmed the importance of the Peru–Chile undercurrent (PCUC) in transporting the ESSW poleward, contributing to the entrance of ESSW into the northern Patagonian fjords. A mooring system installed in the water interchange area between the Pacific Ocean and Patagonian fjords detected a decreasing DO of −21.66 μmol L⁻¹ over 7 years, which was explained by the increase in PCUC transport of 1.46 Sv. Inside the Puyuhuapi fjord system, a second DO time series exhibited more marked deoxygenation with −88.6 μmol L⁻¹ over 3 years linked with the influence of ESSW and local processes, such as DO consumption by the organic matter degradation. The recent deoxygenation registered in the northern Patagonian fjords demonstrates the significance of studying DO in the context of reducing the global oxygen content, further warranting the quantification of the impacts of deoxygenation on life cycles of marine organisms that inhabit the Patagonian fjords and channels and the Humboldt current system.