The implementation of the Water Framework Directive in the system of water resources management in Slovenia and Sweden is the main subject of this thesis. It presents the success of implementation of Directive among the Member States and quality status of surface water and groundwater in European Union. All three phases of the implementation process are presented; there is also time schedule of implementation of measures in every country. Furthermore, there is a description of changes, due to implementation of the Directive, and the role of institutional bodies in water management. The plan of management of catchment area and the programme of measures of both countries is described; there is also the example of management plan of Swedish sub-basin. In the final part are the findings, where are shown the differences as well as weaknesses in the implementation of Directive in the management system of both discussed countries.