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The EU Water Framework Directive (Directive 2000/60 EC) provides numerous requirements, including achievement of good status of all water bodies by 2015. However, meeting this environmental target brings substantial costs. In justified cases, member states may request an extension of the deadline based on disproportionality of costs of meeting the WFD requirements. Definition of disproportionate costs must be based on economic analysis and on the WFD general requirements. This thesis provides a review of proportionate costs in the context of the WFD, identifies main requirements for its practical definition as an exemption and provides a review of foreign methodical approaches to define cost proportionality. It is clear that the Cost-effectiveness analysis (CEA) and the Cost-benefit analysis (CBA) are most commonly used methods to determine the cost proportionality treshold. This thesis discuss the relevance of these methods to define cost proportionality to reach good status of water bodies. The thesis also provides methodology to assess cost proportionality based on modified CBA and analyses ecosystem services of water bodies. In addition, the thesis points out the methodological complications and uncertainties of suggested methodology. Main methodological issues are connected with definition of right scale of analysis and synergy effects of measures, analysis of costs and definition of suitable measures and analysis of benefits and quantification of ecosystem services of water bodies.