Ongoing eutrophication is changing the Baltic Sea ecosystem. Aquaculture causes relatively small-scale nutrient emissions, but local environmental impact may be considerable. We used substance flow analysis (SFA) to identify and quantify the most significant flows and stocks of nitrogen (N) and phosphorus (P) related to rainbow trout aquaculture in Finland. In 2004-2007, the input of nutrients to the system in the form of fish feed was 829 t N year(-1) and 115 t P year(-1). Around one-fifth of these nutrients ended up as food for human consumption. Of the primary input, 70% ended up in the Baltic Sea, directly from aquaculture and indirectly through waste management. The nutrient cycle could be closed partially by using local fish instead of imported fish in rainbow trout feed, thus reducing the net load of N and P to a fraction.