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Abstract Bioassays were undertaken in order to test the response of the natural late-summer inoculum of the phytoplankton of a Patagonian Reservoir to the additional nutrients generated by the production of salmon in cages. The results are discussed in relation to a 7 year study of the reservoir and the possible directions of trophic development. The main consequences of fish farming activities in Alicura are likely to lead to an increase in both nutrient concentrations, algal density and phytobiomass. The composition of the sediment close to the fish farm is affected. With regard to phytoplankton, we observed changes in species composition and temporal changes in their associations. The additional nutrient sources of fish food and faeces from salmonid production create an internal load that leads to a decrease in the N/P, Si/P and Ca/P ratios of the water column. The trophic level of Alicura Reservoir remains unchanged at present and the impact of fish farming operation remains localized.