Policies for mitigating the eutrophication of coastal waters typically focus on reducing land-based emissions. Fish and fisheries management have been suggested as a potentially efficient complementary measure. The purpose of this paper is to investigate the cost-effective achievement of targets for coastal water transparency with the help of adjusted harvesting strategies for predatory fish, biomanipulation of prey fish, and nutrient load mitigation, taking natural variations in water color into account. We develop an empirical steady-state bioeconomic model and apply it to two case areas along the Swedish Baltic Sea. Results show that prey fish stocks, which negatively affect water transparency, are reduced to a minimum in one study area, while an interior solution with a positive harvest is found in the other. Policies targeting fish management can be relevant for locally tailored strategies to mitigate eutrophication.