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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. Plain Language Summary: The South Eastern Pacific (SEP) hosts one of the most extensive oxygen minimum zones (OMZs) of all oceans, covering an area of 9.8 million km2. An OMZ is caused by the decomposition of large numbers of marine organisms which consume oxygen‐poor water circulation, which means that oxygen levels are not replenished. While previous studies on the SEP OMZ were focused on the center and the northernmost areas of the OMZ, research has not focused on how far south the OMZ reaches, and how it connects to bottom waters in the Patagonian fjords. Here, we analyzed temperature, salinity, and oxygen data collected where the South Pacific water meet Patagonian waters. We demonstrate that low‐oxygen waters are transported by the Peru–Chile Undercurrent (PCUC) as far south as the Patagonian fjords. We show that this leads to low‐oxygen in the oceanic‐fjord area and inside the fjords. This deoxygenation was attributed to the increasing southward transport of deoxygenated equatorial subsurface waters by the PCUC. The deoxygenation reported here provides evidence of the association between the SEP OMZ and the fjord systems of Patagonia. Deoxygenation directly impacts marine life, the cycle of greenhouse gases, and ecosystem services for humans. Key Points: In situ data collected from a Patagonian fjord from 2016 to 2022 revealed a trend of deoxygenation in deep watersA combination of modeling and in situ data demonstrated the arrival of the equatorial subsurface water (ESSW) to northern PatagoniaRecent deoxygenation was attributed to poleward transport by the Peru–Chile undercurrent and ESSW [ABSTRACT FROM AUTHOR]