The sustainable use of precious water resources requires effective water management. In the European Union, water management is mainly regulated by the Water Framework Directive (2000/60/EC), introducing an integrated river basin management approach. As a European Union (EU) directive, the legislation needs to be implemented in the Member States, entailing not only legal transposition but also application and enforcement. One major instrument introduced by the Water Framework Directive is the environmental goal achievement obligation of article 4 WFD, containing also a deterioration ban with several exemptions. We compare the transposition, application, and enforcement of the exemption of permanent deterioration (art. 4 (7) WFD) in the context of the environmental goal achievement obligation regime in Lower Saxony (Germany) and the Netherlands. The study rests on a comparative legal analysis of literature, river basin management plans, and jurisprudence. Although based on the same EU directive wording and case law of the European Court of Justice, the deterioration ban and the exemption of permanent deterioration are implemented rather differently. While the deterioration ban is predominantly understood as planning obligation in the Netherlands, it became an important permit requirement in Lower Saxony since the Weser ruling of the European Court of Justice.