The content of the Water Framework Directive (2000/60/EC, WFD) is considerably influenced by its ecosystem approach, stipulating the achievement of a good water status in Europe until 2015. The legal transposition of the ecological requirements into the Federal Water Act has yielded a noticeable greening of German water law. This is not only the result of introducing the environmental objectives and instruments for their achievement into the German legal framework, but also due to their interlinking with the existing legal procedures for water use permissions. However, the interpretation of the European regulations as well as their integration in the system of German water law give rise to a variety of legal questions. They are not only discussed in academia, but gained practical relevance and became subject to court proceedings recently. The paper explains those issues with a special focus on the case of the planned deepening of the river Weser. It is currently pending at the European Court of Justice following a request for preliminary ruling by the German Federal Administrative Court.