The Santa Catarina Island has a mosaic of ecosystems, with great importance for the fishes. There is the presence of estuaries, lagoons, mangroves and sandy beaches in the same island. Thus, the objectives of this study were to evaluate the spatio and temporal fish diversity patterns in estuaries, lagoons and beach systems of Santa Catarina Island, Santa Catarina, Brazil. Fish data collected between 1983 to 2011 in the baía Norte, saco dos Limões, Itacorubi and Ratones mangroves, Conceição lagoon and Índio beach was analyzed. Fish were sampled with different gear techniques. In the North Bay and saco dos Limões individuals were caught by trawl, but in the mangroves and lagoon were used gillnets, cast nets and dip nets. In the Índio beach the fishes were collected using fyke nets. For each local, species accumulation curves were plotted to compare the observed pattern with modelled data, using first order Jackknife estimator. Species richness differences among locals and seasons were tested using PERMANOVA, followed by a canonical analysis of principal coordinates (CAP). To assess the taxonomic structures at each location, the average taxonomic distinctness (AvTD) and the variation in taxonomic distinctness (VarTD) were also used. Higher average species richness was found in the saco dos Limões (mean ± SE; 59.8 ± 2.5), followed by Índio Beach (55.7 ± 2.7), Conceição lagoon (52.3 ± 6.4), North bay (45.0 ± 2.5), mangrove Itacorubi (34.5 ± 3.2) and mangrove Ratones (30.8 ± 3.8). No significate differences for the taxonomic patterns were observed between seasons. Furthermore the hereby data suggest that the fish assemblages of the inner portion of the island of Santa Catarina are mainly formed by estuarine and marine fish, but differing in species richness among locals.