The atoll lagoons are separated from the open sea by a barrier reef, which is covered in some places by islets called "motu" in Tahitian. On most of the atolls, there are openings which enable exchanges of water to take place between the lagoon and the open sea: these passages are called "hoas" in the case of the shallowest channels, and  "passes" when they are navigable. The lagoon waters flow in and out of these openings, depending on the tides and on the sea swell. Many species of fish swim up these connecting channels into the lagoons, where they spend most of their lives, The extent to which the physical and chemical characteristics of a lagoon differ from those of the open sea depend on its degree of aperture.

The lagoon sediments consist of fine sand resulting from the degradation of coral structures, limestone, limestone algae and the shells of the organisms inhabiting the lagoon beds. On the sandy surface, microscopic autotrophic producers (algae and cyanobacteria) are to be found, as well as macroscopic algae and marine plants (phanerogamia). These primary producers are consumed by the heterotrophic animals living either on top of the sediments or buried in the sand. A few centimeters under the surface of the sand, the organic matter is mineralised by various bacterial processes.

In the lagoon waters, autotrophic (primary) production is carried out by the phytoplankton. The latter organisms are ingested by heterotrophic organisms (zooplancton). The bacteria present in the water column remineralise the organic matter and take an active part in the nitrogen and phosphorus cycles.