The Baltic Sea is one of the most eutrophied seas in the world, facing challenges with both hypoxia and algae blooms. In this study we analyse the effect of using different fishery policy instruments to reduce nutrient loads by removing fish biomass from the ecosystem. The study covers Danish, Finnish and Swedish pelagic fisheries. We distinguish between a private optimum maximising the net present value from fishing and a social optimum including the positive externality of removing nutrients. A dynamic bio-economic model, FishRent, is used to estimate the effect of three policy scenarios: Fisheries regulation using individual transferable quotas (ITQ); Economic compensation provided to fishers for reducing nutrients; and Environmental regulation maximising sustainable catches. The results show that the highest social welfare gain is achieved by maximising catch volumes while having a flexible system for quota trade within the fishing sector. The social welfare gain from the positive externality of the extra fish landed in this case outweighs the private loss of not fishing at the optimal individual level (maximum economic yield).