An important objective of fish ecology is to understand pure and shared effects of abiotic, biotic, and spatial predictors of fish assemblages’ structure on continental shelves. This study aims to assess the structure of the bottom-associated fish assemblage on the shallow inner continental shelf of Paraná, southern Brazil, in response to physicochemical, biological, and spatial factors. We hypothesize that this structure is associated with the benthic megafauna, particularly with the distribution of the Brazilian seabob shrimp Xiphopenaeus kroyeri, an abundant fishing resource on the shallow coast of Paraná. We used uni and multivariate analyses to examine the distribution of abundance, richness, and composition of ichthyofauna in the region. Using variance partitioning analysis, we determined the pure and shared effect of spatial (latitude and longitude), physicochemical, and spatiotemporal distribution patterns of crustaceans, echinoderms, and mollusks as potential predictors of the structure of the fish assemblage. The data were obtained monthly from a one-year bottom trawl survey, comprising five transects and four depths (six, nine, 12 and 15 m) in a 60 km long section of the inner continental shelf, under the influence of estuaries. We captured 57578 demersal fish, comprising 37 families and 88 species. The average abundance of fish per haul was 387 individuals at a depth of 6 m, decreasing to 114 individuals per haul at 15 m. Average richness also decreased along the bathymetric profile, from 15 to 10 species per haul. Fish abundance and richness responded positively to a seasonal estuarine discharge pattern that was stronger in summer and autumn. High biomass of juvenile seabob shrimp in shallower regions also explained the higher abundances and richness. The results also suggest the existence of two fish assemblages in the region, associated with the distribution of the megafauna and segregated by depth, water surface transparency, and sediment particle size composition. Despite significant seasonal variations, controlled by precipitation and bottom water temperature, the structure of fish assemblages responded to the pure and shared effects of the three predictive components in all seasons. In particular, local coastal hydrography and the prey-predator relationship between fish and seabob shrimp were ecologically relevant processes for structuring fish assemblages at the inner continental shelf of Paraná. This study highlights the complexity of ecological interactions within demersal fish assemblages and the importance of considering biotic and abiotic factors in understanding fish distribution patterns at the spatial scale of inner continental shelves that are influenced by estuaries.