Aquatic agricultural systems in developing countries face increasing competition from multiple stakeholders operating from local to national and regional scales over rights to access and use natural resources—land, water, wetlands, and fisheries—essential to rural livelihoods. A key implication is the need to strengthen governance to enable equitable decision-making amidst such competition, building capacities for resilience and transformations that reduce poverty. This paper provides a simple framework to analyze the governance context for aquatic agricultural system development focused on three dimensions: stakeholder representation, distribution of power, and mechanisms of accountability. Case studies from Cambodia, Bangladesh, Malawi/Mozambique, and Solomon Islands illustrate the application of these concepts to fisheries and aquaculture livelihoods in the broader context of intersectoral and cross-scale governance interactions.