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Glacial lake outburst floods (GLOFs) in Northern Patagonian Ice Field affecting the Baker River basin have increased their frequency in recent years. To evaluate the impact of a GLOF in the hydrography and biological components of the plankton in the Baker Fjord, we assessed the relative contributions of terrigenous versus marine plankton carbon sources to the particulate organic matter (POM) in the fjord before and after a GLOF in the austral summer 2014. We also evaluated whether terrestrial carbon brought into the fjord by the river may reach higher trophic levels via a deposit-feeding organism the juvenile pelagic Munida gregaria. Over a 10-day period, hydrographic profiles, water samples for POM, and zooplankton samples were collected daily from three stations and two depths along the fjord's inner section. Samples of suspended POM and tissue from M. gregaria were analyzed for stable-isotope composition of carbon (C-13). The GLOF arrival produced a thermal front in the fjord, followed by an oscillation of the pycnocline; an abrupt increase in the total organic carbon content of POM, which was attributed to terrestrial input; and a concurrent peak in the abundance of M. gregaria, suggesting an aggregation response to the GLOF. Understanding GLOF effects on local hydrography, productivity, and food web structure provides valuable insight on the potential responses of fjord ecosystems in general to climate change-induced variability. Given present climatic trends in high-latitude zones, more frequent GLOFs might be expected in Patagonian fjords and channels as well as in other high-latitude basins.