In this paper, the role of nutrient transports between marine basins is investigated for cost-effective solutions to predetermined marine basin targets. The interdependent advective nutrient transports as well as retentions among the seven major marine basins of the Baltic Sea are described by input-output analysis. This is in contrast to prior economic studies of transboundary water pollution that include only direct transport between the basins. The analytical results show that the difference in impacts between transport specifications depends mainly on the openness of the basins, that is, their transports with other basins. The application on Baltic Sea shows significant differences in costs and policy design between the nutrient transport specifications. The reason is that the Sea is characterized by long water and nutrient residence times, so relatively large part of nutrients are transported among basins.