Sediments from the Patos Lagoon Estuary in Southern Brazil and sludge from incoming effluents were assessed for the distribution of polycyclic aromatic hydrocarbons (PAHs). Shallow sediments adjoining the City of Rio Grande were found to be contaminated by PAHs mainly near urban effluent discharge, as well as in the port area. Effluents clustered into four groups according to their sources (sewage, industrial, runoff, and mixed), with each demonstrating different contributions of PAHs to the estuary. There was a predominance of runoff and mixed sources. Navigation activity was the second most important source of PAHs to sediments. The PAHs ratio identified the origin of these contaminants as essentially pyrolytic. The impact of PAHs as a result of uncontrolled disposal or accidental discharge of PAH-rich residues was suggested for several points. These points were primarily near gas stations and motor workshops. In about 30% of sampled sediments, the concentration of benzo[a]pyrene surpassed the Threshold Effects Level adopted for marine environments.