Nutrient loads from inland sources to the Baltic Sea and adjacent inland waters need to be reduced in order to prevent eutrophication and meet requirements of the European Water Framework Directive (WFD) and the Baltic Sea Action Plan (BSAP). We here investigate the spatial implications of using different possible criteria for reducing water-borne phosphorous (P) loads in the Northern Baltic Sea River Basin District (NBS-RBD) in Sweden. Results show that most catchments that have a high degree of internal eutrophication do not express high export of P from their outlets. Furthermore, due to lake retention, lake catchments with high P-loads per agricultural area (which is potentially of concern for the WFD) did not considerably contribute to the P-loading of the Baltic Sea. Spatially uniform water quality goals may, therefore, not be effective in NBS-RBD, emphasizing more generally the need for regional adaptation of WFD and BSAP-related goals.