The complexity and diversity of coastal zones in the tropics makes them challenging to govern. Initiatives to manage terrestrial-ocean fluxes of freshwater, sediments, nutrients and pollutants are mostly local and relatively new. Recent studies of policy processes and institutional arrangements are often critical of the use of scientific knowledge, lack of meaningful stakeholder participation and persistent institutional gaps, but have identified opportunities for better governance. Models and assessment can improve consideration of key social and ecological processes in planning and policy if linked to decision-making processes. Stakeholder deliberation increases shared understanding that can lead to negotiations and agreement on management strategies and actions. Accountable and well-coordinated authorities can improve their management functions over time. Further ecologically informed research on institutions and policy-processes at the land-sea boundary in the tropics is needed. © 2011 Elsevier B.V.