The São Francisco River has historical and economic relevance to the development of Northeast Brazil. However, the dams and reservoirs located along the basin and anthropogenic activities have been affecting its estuary. Herein, 26 surface sediment samples were analyzed to access the origin and distribution of aliphatic hydrocarbons. Concentrations of these hydrocarbons ranged from 0.95 μg g−1 to 2.87 μg g−1 in the summer and from 0.22 μg g−1 to 1.49 μg g−1 in the winter. Diagnostic ratios and indexes indicate higher plants, bacteria, and petroleum as hydrocarbon sources. A positive correlation was also observed between ∑n-alkanes and total organic matter (0.25) and fine fraction (0.47) as well as a significant difference (p < 0.05) between long-chain n-alkanes in the two sampling periods. Although the concentrations found in this study were lower than those in the other impacted coastal zones, our results have indicated the possible presence of petroleum contamination mainly associated with the discharge of oil derivatives from boat activities. •Aliphatic hydrocarbons were investigated in surface sediments from São Francisco river estuary.•The total concentrations of C10 to C34 n-alkanes ranged from 0.22 μg g−1 to 2.87 μg g−1 dw.•Higher plants were considered the main source of aliphatic hydrocarbons related to biogenic inputs.•Petrogenic sources of aliphatic hydrocarbons found in this study were predominantly degraded oil and boat traffic.