Improving risk assessment and remediation rests on better understanding of contaminant bioavailability. Despite their strong toxicological attributes, little is known about the partitioning behaviour and bioavailability of polar polycyclic aromatic hydrocarbons (PAHs) in aquatic environments. The present study provides an insight into the bioavailable fractions of polar PAHs and their parent analogues in the tissues of the Sydney rock oyster, Saccostrea glomerata, a model aquatic bio-indicator organism. The concentration and distribution patterns of parent and polar PAHs including oxygenated PAHs (oxyPAHs), nitrated PAHs (NPAHs) and heterocyclic PAHs (HPAHs) were determined in water, sediment and oysters from an ecologically and economically important estuary of New South Wales, Australia. Total concentrations of PAHs, oxyPAHs, NPAHs and HPAHs were higher in sediments compared to oyster tissue and water. For most polar PAHs, total concentrations for water, sediment and oyster samples were <1 μg/g (μg/l for water) while parent PAH concentrations were several orders of magnitude higher. Computed biota-sediment accumulation factors (BSAFs) on lipid-normalized oyster concentrations revealed that while ∑oxyPAHs and ∑HPAHs exhibited low accumulation from sediment to oyster tissues (BSAF <1), ∑PAHs and ∑NPAH were found to be accumulated at high levels (BSAF >1). BSAF individual computation showed that bioaccumulation of nine investigated HPAHs in oyster tissues were relatively low and only 2-EAQ (oxyPAH) and 1N-NAP (NPAH) showed high levels of accumulation in oyster tissues, similar to parent PAHs. To the best of our knowledge, this is the first known study on the bioavailability of polar and non-polar PAHs in an Australian aquatic environment. The outcome of this study might be a useful indicator of the potential risks of polar PAHs to humans and other living organisms.