This paper reviews of GEF investments and concludes that existing governance and management arrangements could be improved to balance the often diverse and conflicting water management objectives, stakeholder priorities, and institutional arrangements of connected systems in the source-to-sea continuum. This paper presents a conceptual framework to support the design and implementation of GEF projects, addressing inter-connected upstream and downstream water systems by identifying several key flows that need to be managed across the source-to-sea continuum and geographies.