The composition of estuarine fish fauna is dynamic and complex. Despite the variation in fish fauna in estuaries, it is possible to observe some species associated with microhabitats. The assemblage composition of these communities is apparently derived from habitat selection. The aim of this study was to assess the structure of the demersal fish fauna of the Paranaguá Bay and its relationship with biotic and abiotic factors. To this end, monthly collections were conducted using an otter trawl, from October 1999 to September 2000, at five sites in the shallow infralittoral. Biotic (organic matter, and invertebrates) and abiotic factors (salinity, temperature, pH, dissolved oxygen, seston, and nutrients) were recorded during sampling. A total of 6,623 individuals were captured, belonging to 2 species of Chondrichthyes and 53 species of Actinopterygii (26 families). Sciaenidae was the most representative in terms of richness, with 11 species, and Ariidae was the most representative in terms of abundance. The catfish Cathorops spixii was the most abundant species, representing 21 % of the entire catch. There were significant differences in the composition and abundance of the fish fauna among the studied areas, as evidenced by the Shannon-Wiener diversity index. Such differences seem to be related to the complexity of habitats, which occur due to different types of bottom cover found at each sampling site. The abiotic variables indicated little influence on the structure of the fish assembly. These results contribute to a better understanding of the fish fauna from the shallow infralittoral areas of the Paranaguá Bay, and provide data to decision makers for better implementation of management and conservation measures.