From December 2005 to November 2006, 216 samples were taken from the main channel of the Goiana Estuary, representing a total sampled area of 23 ha. Ariidae species were the most abundant in density (1600 individuals ha−1, 53%) and biomass (18 813 g ha−1, 63%). Cathorops spixii was the most abundant in density (1340 individuals ha−1) and biomass (14 203 g ha−1). The variables: number of species, total density and biomass, showed significant interactions between the factors of areas and seasons (P < 0·01). The highest total density (7394 individuals ha−1) and biomass (70 292 g ha−1) occurred in the middle and upper estuaries, respectively, during the early-rainy season. The density of C. spixii differed significantly between areas and seasons (P < 0·01), while Cathorops agassizii differed significantly only between seasons (P < 0·01). The biomass differed significantly for the species C. spixii, C. agassizii and Sciades herzbergii between seasons, and C. spixii and C. agassizii between areas. Also, the density and biomass of C. spixii and C. agassizii showed interaction between areas and seasons. Only the biomass of S. herzbergii showed interaction between areas and seasons (P < 0·01). This indicates that seasonal variations influenced the distribution of Ariidae species in the different areas of the Goiana Estuary. Moreover, canonical correspondence analysis highlighted a strongly significant correlation (P < 0·01) between the seasonal variations of the environmental gradients (salinity and water temperature) and distribution of catfishes. The management and conservation of estuaries should take into account the life cycle of these species in different estuarine areas and hydrological seasons.