Estuaries are highly productive coastal ecotones. Influenced by tidal, wave, and wind actions that control water mixing. Estuaries recipients of allochthonous organic matter (OM). OM is processed and exported to ocean under high-flow conditions(Borges,2005). Estuaries regulate the quantity and quality of OM that reaches the ocean (McCallister, etal.2006). Anthropogenic activities in the coastal region are changing the ecological integrity of the coastal system (Rabouille et al., 2001).