The implementation of the EU Water Framework Directive and the achievement of its water quality objectives will to a large degree depend on scientific knowledge about the sources and status of water resources and the effects of mitigative measures. Coastal waters will be of central interest, since the management of whole river basins may be affected if coastal water status is not satisfactory. The Water Directive's general directions on what information the water authorities need and on suitable methods for obtaining such information leave it to the Member states to decide on more precise instructions. Improved legal mechanisms are needed to assist and guide the managers and scientists charged with implementing the directive and achieving its water quality objectives, particularly when faced with insufficient information, flawed knowledge, or changed circumstances. We assess progress in the current process of implementing the Water Directive in Sweden, focussing on coastal waters, and on general problems arising using this type of legal technique.