This report presents the results of the GIWA assessment of the Colombia & Venezuela and Central America & Mexico sub-systems – located in GIWA region 3, the Caribbean Sea. The regional team identified habitat and community modification as the priority concern of both sub-systems. In the Colombia & Venezuela sub-system, coastal habitats are being degraded by a multitude of issues, particularly land-based sources of pollution. The transboundary ecosystems of the Central America & Mexico sub-system have been severely degraded as a consequence of agricultural and urban expansion, increased pollution loads and unsustainable forestry practices. The past and present status and future prospects of these issues are discussed, and they are traced back to their root causes. Feasible policy options are proposed that target key components identified in the Causal chain analysis in order to minimise future impacts on the transboundary aquatic environment.