Polycyclic Aromatic Hydrocarbons (PAHs), a family of chemical compounds formed during incomplete combustion or in high-temperature pyrolytic processes involving fossil fuels, are deposited in aquatic sediment from a variety of sources. The hydrophobic nature of these tracer compounds provides a good understanding of their transport in the environment. Parent PAH ratios and principal component analysis-multiple regression models can be used to apportion the sources of sediment PAHs. These tools were tested for 12 USEPA priority PAHs measured from the sediment samples of two adjacent aquatic environments, the Gulf of Gemlik and Lake Iznik. The level of sediment PAHs was closely related with riverine/terrestrial and atmospheric inputs, together with seaport and fishing activities. The highest level of anthropogenic inputs was dominated along the highly-populated eastern and southern coasts of the Gulf of Gemlik. On the basis of principal component analysis and various PAH ratios, the majority of sedimentary PAHs in front of the main industrial-tourism ports and anchoring areas in the Gulf of Gemlik originate from pyrogenic sources together with petrogenic PAHs. A mixed pattern of pyrolytic and slightly petrogenic input of PAHs can be observed at the coastal parts of the Lake Iznik influenced by riverine inputs where the contribution of unburned petroleum sources was higher. An important contribution of atmospheric inputs was detected for both cases, due to heating with coal, petroleum coke particles and biomass burning from various sources.