The Cabiúnas Lagoon is a narrow water body that is perpendicular to the sea and isolated from it by a sandbank. Before 1991, the sandbank was sometimes opened for a few days by local residents, but at present seawater only enters by limited groundwater seepage or by overtopping the sea barrier in storms. In 1998 the Restinga de Jurubatiba National Park was established, including the Cabiú nas Lagoon. Studies on the structure and spatial distribution of the fish assemblage were performed between 1991 and 1994; we carried out one year (2001–2002) of monthly monitoring of the lagoon to identify spatiotemporal variations in the lagoon fish assemblage. The closed sandbank altered salinity content, and favoured oligohaline conditions and the increase of the aquatic macrophyte abundance, promoting freshwater species dominance and reduction of the marine dependent and some coastal lagoon resident species of fish adapted to paralic ecosystems. Two freshwater, two coastal lagoon resident, and five marine dependent fish species, which had been registered in the first studies (1991 and 1994), were not captured in the subsequent samplings. The mean number of individuals (N m−2) decreased significantly (Kruskal-Wallis [KW] = 9.977; p = 0.0068); the decrease in biomass was found to be 80%. Species richness and diversity were also significantly reduced. Differences in the current conditions regarding specific composition along the longitudinal axis of the lagoon were observed. Temperature, salinity, and macrophyte coverage were important variables that influenced fish spatial distribution, abundance, and biomass.