The presence of polycyclic aromatic hydrocarbon (PAH) compounds in sediment and water samples collected in the estuary area of Paranagua, southern Brazil, was investigated. There is a lot of port activity in the region. Recreational fishing is widespread; thus, there is concern about possible contamination by PAHs. The 16 priority PAHs were investigated, and only eight were found. The total concentration of PAHs ranged from 40.8 to 406.8 ng/g. High molecular weight were the most abundant, while PAHs with a low molecular weight were absent. There are suspicions that the main source of PAHs is combustion, but some uncertainties exist, and there may even be the presence of PAHs resulting from accidental spills of crude oil. Although the sediments contain PAHs, the amount is below the maximum concentrations allowed by the Brazilian environmental legislation, as well as the maximum levels at which adverse effects are observed. From the analytical results, a probable bioaccumulation was assessed in the local trophic chain using a mathematical model (Arnot and Gobas, Environ Toxicol Chem 23(10):2343-2355, 2004). The model showed that there is a possibility of biomagnification along the food chain selected. Three fishes with high local consumption were selected, and the concentration of some PAHs could be found in those fishes.