To test whether deforestation of tropical forests alters coupling of watersheds, estuaries, and coastal waters, we measured nutrients in 8 watershed-estuarine systems on the Pacific coast of Panama where watershed forest cover ranged from 23 to 92%. Watersheds with greater forest cover discharged larger dissolved inorganic nitrogen concentrations and higher N/P into estuary headwaters. As freshwater mixed with seawater down-estuary, within-estuary biogeochemical processes erased the imprint of watershed deforestation, increased ammonium, lowered nitrate concentrations, and otherwise altered down-estuary water column composition. As estuarine water left mangrove estuaries, ammonium, nitrate, and phosphate, but not dissolved organic nitrogen, were exported to receiving near-shore waters. Mangrove estuaries in this region thus provide important ecological services, by uncoupling coastal waters from changes in terrestrial land covers, as well as by subsidizing adjoined receiving coastal waters by providing nutrients. The pattern of land-sea coupling and exports was disrupted during La Niña-influenced conditions. In one instance when La Niña conditions led to upwelling of deeper layers, high concentrations of marine-derived ammonium were inserted into estuaries. In another instance, La Niña-associated high rainfall diluted nutrient concentrations within estuaries and lowered salinity regionally, and the fresher upper layer impaired coastal upwelling. Regional rainfall has increased during the last decade. If La Niña rainfall continues to increase, disruptions of current land-estuary-sea couplings may become more frequent, with potentially significant changes in nutrient cycles and ecological services in these coupled ecosystems.