The EU Water Framework Directive stipulates that all EU waterways shall have good chemical and ecological status by 2027. Methodologies are described for how to assess and classify waterbodies and make 7-year management plans. Aquatic risk assessment methodologies and environmental quality standards are defined and a biotic ligand model methodology is available to assess the influence of water chemistry on the ability of aquatic organisms to take up metals. Aquatic status classification practices of naturally occurring river basin-specific metals are discussed, specifically how Cu and Zn water quality criteria guideline values have been adopted and defined for Swedish coastal and estuarine waters and how well they represent possible ecological risks. Calculations of bioavailability and ecotoxicity are conducted using recognised models for the Strommen-Saltsjon water body in Stockholm, in which naturally occurring metals, especially Cu, have among the highest background concentrations of Sweden. Proposals are made to improve risk assessment methodologies to better reflect the vitality of living organisms, and to what extent current levels of these metals in Swedish waterways may influence their welfare. The study concludes that a more local assessment including, e.g., studies of the benthic fauna would be relevant for ecological status classification.