The Water Framework Directive (WFD), whose basic aim was to create a legal back-ground for water bodies’ protection, undoubtedly affects all economic sectors. Being a specific and distinctly different water user, agriculture will have the greatest share in the implementation of WFD out of all sectors of national economy. This results from its special character (60% of the country area used by agriculture), large volume of water consumed by evapotranspiration, diffuse pollution etc. Implementation of WFD will call for undertaking of many activities to restrict an unfavourable im-pact of agriculture on water resources and water related ecosystems. It is assumed that agriculture should also protect water resources. Accomplishment of this task imposes significant changes in the land use of river basins. Water management can be an essential factor deciding about the sustainable development of rural areas and biological diversity of agricultural landscape. Actions undertaken so far to implement the WFD are mainly limited to the protection of water quality from agricultural pol-lution. It is also necessary to undertake implementation of other aims of WFD. This refers especially to the provision of good hydromorphological status of water bodies, protection of water related eco-systems and effective water use.