Coastal lagoons worldwide are very dynamic complexes where both ocean and land events are important drivers; any modifications in either of these will have an impact in the coastal waterbody. Coastal lagoons often present problems due to human induced alterations to their hydrosedimentary flows. In this study, a diagnosis was made of the sedimentation problems in the Chantuto-Panzacola coastal lagoon complex. A physical diagnosis was made using hydrodynamics and physical characteristics, followed by computational simulations. Then an ecological diagnosis was performed, using satellite imagery, databases and field data. This was followed by a socio-economic diagnosis and an evaluation of the ecosystem services the lagoon system provides. A severe sedimentation problem was found following the diagnosis and using the Revised Universal Soil-Loss Equation. It was established that a relationship exists between the sedimentation of the coastal lagoon complex and erosion in the upper watershed. Three options were proposed: No action, dredging and reforestation. A brief cost/ benefit analysis was made for each alternative and the reforestation alternative was seen to be the most feasible and environmentally sensitive. The benefits of reforestation will not only be reaped within the lagoon complex, but also in the high watershed, where there will be fewer landslides and lower vulnerability to erosion.