The United Nations Environment Programme (UNEP) as part of the UNDP/UNEP Global Environment Facility (GEF) IW:LEARN program and numerous partners held the first Global Environment ‘GEF International Waters Science Conference 2012’(GEF IWSC 2012) in Bangkok, Thailand. The three days conference provided a science-policy interface to strengthen the role of science in the management of water systems at the global, regional and local level. The focus was on emerging issues and critical challenges, and highlighting the scientific findings of GEF International Waters (IW) projects.