Ecological guilds have been widely applied for understanding the structure and functioning of aquatic ecosystems. This study describes the composition and the spatio-temporal changes in the structure of the fish fauna and the movements between the estuary and the coast of a tropical estuary, the Itapissuma/Itamaracá Complex (IIC) in northeastern Brazil. Fish specimens were collected during the dry and rainy seasons in 2013 and 2014. A total of 141 species of 34 families were recorded. Almost half of the species (66 species, 47%) were exclusive to the estuary and 50 species (35%) to the coast; 25 (18%) were common to both environments. Marine species were dominant in both richness and biomass as they explore the environment during part of their life cycle, whereas estuarine species were dominant in abundance. Marine stragglers displayed a higher richness, abundance and biomass in the coastal waters. The estuarine environment was dominated by zoobenthivores in terms of richness, while detritivores prevailed in abundance and biomass. Zoobenthivores had the highest richness and abundance in coastal waters, while piscivores had the highest biomass. The IIC supports a rich fauna with a diverse trophic structure and is an important feeding and development area for migratory species.