The Water Framework Directive (WFD) is the most substantial piece of EC water legislation, to date. The WFD sets out a timetable for the implementation of requirements for EU member countries. The candidate countries like Turkey will also adapt the directive and prepare an individual implementation plan. According to 2006 Progress Report of Turkey, EU reported that limited progress on the implementation of WFD is observed in Turkey. It also reports that significant efforts are needed in order to achieve full compliance and implementation by accession. The implementation process of WFD has recently started in Turkey. The process raises a number of shared technical challenges in Turkey having one of the largest surface areas as the candidate among member countries. Turkish water authorities have completed the determination of the river basin structure of Turkey. Regarding the implementation of WFD and the adaptation of water related EU directives, Turkey has made an effort to establish new legislations. However, many of Turkish river basins are transboundary and some of them are shared by Middle East countries. This situation makes harder to establish rational watershed management plans when compared to other transboundary river basins in Europe. Although there is a strong legislative background, environmental infrastructure of Turkey is still lacking and this increases the cost of application of the directive. The total cost of environmental investments for the implementation of all EU legislations is estimated as 50 billion Euros of which the implementation of WFD will constitute the big portion, however, Turkey, is planning to implement the directive by reasonable delays. This paper discusses the efforts for the implementation of WFD and points out the existing and probable complications which can occur throughout the implementation process in Turkey.