Estuary is a water body that have permanent contact with the sea, where the salinity is variable because of the freshwater from drainage basin contribution. The subject is to identify the principal trophic levels in the estuary of the Lagoa dos Patos, one the largest coastal lagoon of the world, situated at south of Brazil. The freshwater flux and sea water intrusion establish physical and chemical characteristics that control the ecological processes making the plankton transport into to the estuary. The estuary of Lagoa dos Patos play an important role in the first stages of life cycle of a variety of fish species, functioning like a nursery to marine and estuary species.

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