Concentrations of polycyclic aromatic hydrocarbons (PAH) were studied in 36 sediment samples collected from 29 sites in the central Adriatic Sea. The total concentration of PAH showed high variability, ranging from 42.85 µg kg−1 in open sea sediments to 28,662 µg kg−1 in the sediments of Šibenik Bay. Unsubstituted, parent PAH were dominant PAH compounds in the entire area of Šibenik Bay and most of the stations in the coastal area. In Kaštela Bay, methyl PAH concentrations were higher than the concentrations of unsubstituted PAH, whereas in the sediments along the mid-Adriatic transect, similar concentrations of both PAH fractions were determined. PAH sources were investigated by applying the Positive Matrix Factorization software developed by the U.S. Environmental Protection Agency (USEPA). The results indicate the presence of four sources, two of which can be considered petrogenic and two pyrogenic. The contribution of the sources to the total concentration PAH at each station indicates the dominance of pyrogenic sources in Šibenik Bay and at most stations in the coastal area. In the sediments along the mid-Adriatic transversal, as well as in Kaštela Bay, PAHs originate mainly from petrogenic sources. The obtained results show that PMF can be a suitable tool for control of PAH pollution and thus, for the management of various activities in the Adriatic region. Seasonal differences between the contributions of sources in the Kaštela and Šibenik bays indicate that the contribution of traffic to the total concentration of PAH was higher during the tourist season. The carcinogenic risk of PAH determined by toxicity equivalent (TEQ) calculations showed an increased carcinogenic risk in the whole area of Šibenik Bay, regardless of the number of PAH compounds considered for the calculations. A low PAH-related carcinogenic risk was found for the rest of the study area.