The 16 priority PAH were determined in sediment samples from the insular zone of Guajará Bay and Guamá River (Southern Amazon River mouth). Low hydrocarbon levels were observed and naphthalene was the most representative PAH. The low molecular weight PAH represented 51% of the total PAH. Statistical analysis showed that the sampling sites are not significantly different. Source analysis by PAH ratios and principal component analysis revealed that PAH are primary from a few rate of fossil fuel combustion, mainly related to the local small community activity. All samples presented no biological stress or damage potencial according to the sediment quality guidelines. This study discuss baselines for PAH in surface sediments from Amazonic aquatic systems based on source determination by PAH ratios and principal component analysis, sediment quality guidelines and through comparison with previous studies data.