Turkey has a natural heritage of marine and inland waters and doubtlessly should be considered as a wealthy country having the resources and services provided by them. Turkey has got 48 natural lakes above 5km2, having a total surface area of 8,900 km2. This makes an important fresh water reservoir where the world’s water resources are getting limited day by day. The changing precipitation regimes and the pressures exerted on lakes have globally created the decline of both the quality and quantity of waters. The main reasons of pollution at the lake reservoir areas are intense urbanization and untreated waste water discharges and industrial activities. In addition, wrong strategies of agricultural irrigation, deforestation and erosion have impacts on the reservoirs and they accelerate the decline of the quality of lake ecosystems. This leads to the disappearance of commercial species as well as the natural habitats. The rehabilitation of destroyed ecosystems is very costly. Turkey also has a long coast of about 8300 km and with its territorial marine waters (12 nm) as well as economic exclusive zone area (in the Black Sea) and the inland sea (Marmara Sea), it has got a considerable marine area. Seas embrace living and non-living natural resources providing ecosystem services, jobs and enhancing economic activities like fisheries, transport, energy, food, tourism and regulate climatic factors. Especially, the coastal waters similar to the fresh water reservoirs are under the heavy pressure of land-based activities and facing the threats of pollution, eutrophication and biodiversity loss. The scientific evidences of these and the environmental data are available for most coastal area. However, in order to assess the status of marine waters and the impacts of the sea- and land-based pressures on the marine ecosystems, we do not have enough information and scientific findings. So the MIW SBU is contributing to increase the necessary knowledge to assess the quality of the marine and inland waters, to protect them and to enhance the sustainable management of their resources.