This study aims to understand the economic and bio-physical conditions under which mussel farming is a cost-effective mitigation measure to improve water quality related to excess nitrogen in fjords and coastal areas. We set-up a mixed-integer optimization model including every farm in three agricultural catchments surrounding Limfjorden, the largest fjord in Denmark. We include a number of relevant nitrogen abatement measures, including agricultural land-use measures and mussel farming in the sea. The aim is to model the least costly combination of mitigation measures to improve water quality when agricultural, environmental and market conditions vary. We run three scenarios varying environmental conditions for mussel productivity and market opportunities for mussel-based products as organic animal feed. We analyze the resulting marginal abatement costs and draw insights about the potential scale of mussel farming for the different catchments. We show that mussel farming is a cost-effective option for 2 of the 3 catchments, but that decreasing mussel productivity over time may make the measure ineffective for one of the catchments, if a market for feed is not available. The possibility of a market for mussel-based organic feed significantly increases the share of nitrogen reduction done by mussels and decreases overall costs by up to 65%. Ultimately, the results indicate that, for catchments where environmental conditions are adequate, mussel farming can be a cost-effective nutrient reduction measure. Therefore, mussel farming can potentially increase the cost-effectiveness of incentive schemes aimed at reducing eutrophication in fjords and coastal waters.