During GEF-3 the GEF provided grants through the operational programs (OPs), three of which were in the International Waters focal Area.

• Waterbody-based Operational Program
• Integrated Land and Water Multiple Focal Area Operational Program
• Contaminant-Based Operational Program

The OPs have been superseded by the GEF Focal Area Strategies (GEF-4 and GEF-5).