The construction of dams causes changes in river variables, as a result of direct changes in their hydrological and biogeochemical cycles. One of the most notable changes is the flow regulation, which reduces seasonal events and the hydrostatic pressure exerted by freshwater, increasing the saltwater wedge intrusion into the system. Changing the salinity regime causes modifications in downstream ecosystems as well as in the distribution and composition of the fish fauna. In Brazil, the São Francisco River stands out, which has a system of cascading dams, built between the 70’s and 90’s. Because of these changes caused in the natural course of the river, this study aimed to analyze the patterns of composition and occurrence of the ichthyofauna at the mouth of the São Francisco River and relate them to the physical and chemical variables of the region. In order to evaluate the patterns of composition and occurrence of the fish fauna at the mouth of the São Francisco River, monthly trawls were conducted along the bank and physical and chemical variables were analyzed in the river channel over a period of one year. The relationship between abundance and species richness with environmental variables was verified using Generalized Linear Models. A total of 101,958 fish belonging to 87 taxa were caught, with emphasis on marine fish, both in number of individuals (99.92%) and in biomass (99.31%). A spatial gradient was detected, in which sites 1 and 2 were under marine influence, sites 3 and 4 represented the transition between the environments and site 5 was under the influence of brackish and freshwater. In general, the effect of the São Francisco River dams on the fish fauna was observed, with a predominance of fauna with more estuarine and less freshwater characteristics.