Turkish coastal waters and areas are harboring a great potential of tourism and other socio-economic activities besides its natural beauties and also are under the pressures of these activities. In TUBITAK’s National Water R&D and Innovation Strategy (2012-2016), the environmental targets regarding the chemical, physiochemical, biological and hydromorphological quality of all surface waters including the coastal and transitional waters have been set. In this framework, the studies on the quality of receiving water bodies have been conducted and the methods and tools for the identification of discharge criteria of industrial effluents are identified. In addition to that, in the frames of EU-Marine Strategy Framework Directive (2008) it is required to identify targets of “good environmental status (GES)” for eleven descriptors of GES and to achieve them at the European and regional seas (Black Sea, Mediterranean). Within the context of regional cooperation, Turkey has also considered to work on the GES targets and indicators. A similar approach had previously been adopted for the coastal and transitional waters with the EU-Water Framework Directive (2000) setting the targets for “good” ecological and chemical status. However, neither in our coastal waters nor in marine waters there is enough data to make such assessments and classifications. Long term monitoring data is usually required to establish reliable indicator based assessments. Nevertheless, in order to apply effective and sustainable management strategies, knowing the ecological status and the environmental quality of coastal and marine waters is distinctly important. Therefore, the “Marine and Inland Waters research group” have performed studies on the monitoring of marine and coastal seas, ecological/environmental quality classification of costal and marine waters and the identification of feasible action plans to achieve the identified targets of “good” status.