The Global Environment Facility (GEF) has catalysed the largest investment of its kind in human history into shared water bodies. The GEF has catalysed more than US$7 billion of investment in managing shared waters – fresh and marine – in almost every part of our planet, above and below its surface. The crucial role for science and scientific discovery in determining the nature and priority of investments has largely been taken for granted and its role and full potential have not previously been scrutinised. The present report is the culmination of a process that seeks to raise the profile of use and generation of science in the GEF International Waters (IW) portfolio and ensure that scientific advice is truly fit for purpose, gives greatest added value and that the science emerging from GEF projects contributes to our global knowledge base. In the IW:Science process, we have examined projects focussing on transboundary ground waters, rivers, lakes, coastal areas, large marine ecosystems and the global ocean and distilled the lessons learned in a series of synopsis reports and finally into the present document.