This article discusses two legal issues that relate to the conflict between the interest of protecting habitats and species under the Habitats and Birds Directives, 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 possible conflict between the protection rules of the Habitats and Birds Directive on the one hand and the Renewable Energy Directive on the other hand, and second, the lack of integration between the Renewable Energy Directive and the derogation clauses of the Habitats and Birds Directives. Tidal stream energy is used as a case study to show the practical relevance of the legal issues for the large-scale deployment of innovative water-related renewable energy techniques. The final sections discuss solutions to the legal issues. These are first, the application of adaptive management in combination with mitigation or 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 Habitats and Birds Directives and the Renewable Energy Directive. The final sections also discuss the applicability of the findings of this article to other innovative water-related renewable energy sources such as wave energy and salinity gradient energy (blue energy).