This article discusses two legal issues that relate to the conflict between the interest of protecting water quality under the Water Framework Directive (wfd), versus the interest of promoting the use of innovative water-related renewable energy, with regard to the quota in the Renewable Energy Directive. These legal issues are: first, the conflict between the provisions of the wfd and the Renewable Energy Directive as expressed by the no-deterioration obligation, and second, the lack of integration between the Renewable Energy Directive and the derogation clause of the Water Framework Directive. Tidal energy and salinity gradient energy (blue energy) are used as a case study to show the practical relevance of the legal issues for innovative water-related renewable energy techniques. The final section discusses solutions to the legal issues. These are first, the application of adaptive management in combination with phased deployment in order to deal with uncertainty, and second, the introduction of detailed renewable energy plans per Member State in order to increase integration between the wfd and the Renewable Energy Directive.