The Water Framework Directive aims to achieve ‘good status’ for all water bodies in the European Union. However, exemption clauses enable member states to delay protective measures and to lower water quality objectives. The ambiguity of exemption clauses has led to a plurality of approaches across the continent. They differ as to their political objectives, i.e., the overall ambition displayed in implementing the Directive, and to their methodological choices, i.e., the analytical tools used to justify exemptions. This article argues that those political and methodological dimensions influence each other. Relying on a framework of analysis that integrates key recommendations from the literature, we explore the usage and justification of exemptions in two countries, the United Kingdom and France. Our analysis suggests that analytical methods were often decided so as to reflect the ecological ambitions of a country, and some methodological choices seem to have had unintended consequences for water quality objectives. We conclude that economic methods should be adapted so that they take into account, rather than ignore, the political ambitions of a country in the field of water.