Estuaries are coastal regions where fresh and marine waters mix. They are characterized by tidal intrusion or brackish water, and consist primarily of lower channels of rivers. They are affected by daily tidal variations.

Nine of the island's 46 rivers that empty into the ocean have true estuarine zones. The lower channels of these rivers, which are typically only 5-20 m wide and 1-4 m deep, have elevated salinity levels that extend 0.5-1.6 km upstream (Wilder, 1976). The most common indicator plant of river zones with brackish water regimes is Nypa fruticans.

Estuarine areas are important habitats for juveniles of many fish species, including jacks, snappers, and surgeonfish. They are also important habitat for adults of many species of rabbitfish, snappers, and several other families of fish. Several types of fish and other aquatic organisms are found only in this type of habitat, including ponyfish, mudskippers, many species of crab, oysters, and snails.