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In the context of the Water Framework Directive, the French Water Agencies were asked to justify exemptions, for disproportionate cost reasons, to the “good water” status in a series of river basins in 2015. The ministry of the Environment and the economists of the Water Agencies agreed on the fact that this justification would be based on cost-benefit analyses. A great number of costbenefit analyses were carried out on water bodies or groups of water bodies. This article reports on this experience conducted by the French Water Agencies. It highlights the fact that the large majority of restoration projects generated higher costs than benefits. It suggests that the implementation of the Water Framework Directive could be considerably limited by the use of the Costs-Benefits-Analysis. This result is discussed, especially with regard to the assessment of non-market benefits. These methods are in fact a source of much technical uncertainty which can be used in a strategic way to justify lack of implementation of the EU Directive. Last, the article questions the limits of economic referentials against the legal referential in the implementation of environmental policy.