The increasing occurrence of harmful algal blooms (HABs) affecting mariculture has been related to climatic factors but also to increasing eutrophication of coastal zones, to which aquaculture may also contribute. The role of climate change on HABs may be increasingly relevant but scientific efforts to separate this from other causal factors are to date inconclusive. HABs have been a permanent threat to the aquaculture industry in southern Chile, yet government and farmers may have not paid enough attention to scientific information and advice, even when risk-based predictions and warnings have been provided. Here we describe eutrophication risk assessments for water bodies hosting salmon farms and climate change risk maps for the salmon industry in Chilean Patagonia, including the increase of HABs as a main threat. Assessments and maps were delivered in 2020 both to producers and to government. We show that such risk information and mapping could have lessened recent salmon mortality due to HABs (March-April 2021) if government and farmers had followed explicit recommendations to reduce salmon farming production in water bodies with higher risk. This measure would reduce Exposure and Sensitivity under the climate change risk framework used. We provide policy recommendations, including reviewing maximum salmon production in relevant water bodies such as fjords according to eutrophication risks, while paying attention to additional stress from climate change variability and trends.