Since its creation in 1991, GEF has funded more than 500 projects in 120 countries. 165 nations participate in GEF and form the GEF Assembly. GEF's Governing Council is made up of 16 representatives from developing countries, 14 from developed countries, and two from economies in transition. All decisions on project funding are made by the Council.

The UN Development Programme (UNDP), the UN Environment Programme (UNEP), and the World Bank are GEF implementing agencies. UNDP is primarily responsible for implementing technical assistance and capacity building programmes, and also manages the Small Grants Programme aimed at enabling NGO involvement. UNEP takes the lead in advancing environmental management at regional and global levels within GEF-financed activities and in catalyzing scientific and technical analysis. UNEP also administers and supports the GEF Scientific and Technical Advisory Panel. The World Bank helps to develop and implement investment projects, seeks to mobilize resources from the private sector, and acts as trustee for the GEF Trust Fund.

GEF funds projects in four programme areas: Climate change. Biological diversity. The ozone layer. International waters. GEF is the leading multilateral entity working to reverse the degradation of aquifers, basins, lakes, oceans, rivers, and wetlands of international significance. So far, over 240 million USD have been allocated to international waters initiatives that help address shared problems in a co-ordinated, cost-effective manner in, inter alia, China; the Philippines; the Molucca Straits; the Eastern Caribbean; Senegal; Mauritania; the Black Sea; the Danube River Basin; the Gulf of Guinea; the Red Sea; the Aral Sea; the Caspian Sea; the Pacific Coast of South America and Central America; and Lake Victoria.

In the GEF Operational Strategy, four major areas of concern related to international waters are identified: Degradation of the quality of transboundary water resources; Physical habitat destruction; Introduction of non-indigenous species; Excessive exploitation of living and non-living resources. Long-term operational programmes within this focal area are a waterbody-based programme; an integrated land and water multiple focal area programme; and a contaminant-based programme. These will ensure that different types of international waters geographic settings are addressed; that the land degradation cross-cutting theme and linkages with other GEF focal areas receive attention; and that a more complete range of imminent threats is covered.