The Itajaí-Açu estuarine system, located in southern Brazil, has great economic importance due to the presence of two ports (Itajaí and Navegantes). This system is affected by industrial and dredging activities, which can cause the remobilization of pollutants accumulated over time in the sediment. In this context, hydrocarbons were assessed in twelve surface sediment samples. n-Alkane and polycyclic aromatic hydrocarbons (PAH) concentrations were determined by gas chromatography and their sources assessed. Total concentrations ranged between 0.50 ± 0.04 and 69.70 ± 3.90 µg g -1 dry weight (d.w.) for n-alkanes and from 63.9 ± 12.1 to 1459.0 ± 43.5 ng g -1 d.w. for PAH. Most of the sediment samples presented carbon preference index (CPI) values close to unity, indicating that the area is submitted to petroleum-related sources, mainly close to Itajaí harbor, where an intense unresolved complex mixture (UCM) was observed. The presence at all stations of aβ-hopane biomarkers also indicated petrogenic input. Based on selected PAH ratios, the sedimentary PAH composition reflects a mixture of both petrogenic and pyrolytic sources. A comparison of the PAH concentrations found in this study with those listed in the sediment quality guidelines (SQGs) indicated that adverse biological effects on the biota are rarely expected.Keywords: aliphatic hydrocarbon, polycyclic aromatic hydrocarbon, biomarker, hopane, contamination IntroductionContamination levels in coastal environments are increasing mainly due to the presence of anthropogenic activities, as waste industrial discharges, industrial activities, navigation traffic, etc.1 Therefore, sediment contamination in such areas may occur. In several countries, port activities are rapidly developing, requiring greater attention, especially in relation to the dredging of contaminated sediments and environmental management. 2,3The Itajaí-Açu estuarine system is located on the north-central coast of Santa Catarina state, in Brazil. This is an area of economic interest not only because of tourism, but also due to the presence of the Port of Itajaí, which is considered the third largest container handling port in Brazil, the major international trading point of the state, and the largest national fishing pole landing site. Associated with this latter activity, several fish processing industries are installed along the margins of this estuary, mainly in the city of Itajaí. These industries dispose their waste products, usually without any treatment, directly into the estuary. [4][5][6][7] In addition, the harbor area is constantly dredged, in order to maintain the navigation channel at an elevation of 11 meters. In May 2011, dredging began to deepen the main river channel, aiming to increase the depth from 11 to 14 meters, allowing the entrance of larger ships. Sediment dredging can cause remobilization of the pollutants accumulated in this compartment over time. 6 O r g a n i c c o m p o u n d s s u c h a s a l i p h a t i c hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (P...