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Abstract The growth of Chilean salmon production has not been free of important sanitary and environmental shortcomings. To ensure sustainability, it is necessary to understand the environmental impacts of salmon production on the Patagonian ecosystems. Currently, there is limited regulation or monitoring of impacts in the freshwater phase compared to the marine fattening stage, and there is some evidence of local eutrophication impact and diversity changes downstream the farms. Eutrophication of Patagonian channels and fjords from marine farms has been recognized as crucial environmental risk, although most scientific evidence comes from local effects below and around farms. So far, there are no regulations based on carrying capacity estimates to limit maximum fish biomass per area or water body. There is controversy regarding the potential role of nutrients derived from farming in triggering harmful algal blooms, yet current environmental monitoring and available information does not allow establishing or rejecting a cause–effect relationship. Pesticides used to control sea lice infestation have been shown to be deleterious to some non‐target species. There is evidence that the use of high quantities of antibiotics has allowed the development of antibiotic‐resistant bacteria in sediments and there is concern that salmon aquaculture has the potential to increase the proportion of antimicrobial‐resistant bacteria to antibiotics that are used in human medicine. There is an urgent need for more comprehensive ecosystem (beyond farm) studies on the impacts of antibiotics. Escapes of salmon (exotic species) from farms are a relevant environmental risk, although the most farmed species, Salmo salar , has shown little success in establishing wild populations. The review identifies critical knowledge gaps whose fulfilment is essential to advance towards an ecosystem approach to aquaculture and to protect Patagonian ecosystems.