This reconnaissance study was undertaken in 2012 to examine the occurrence of common perfluoroalkyl substances (PFAS), including perfluoroalkyl sulphonic acids and perfluoroalkyl carboxylic acids in rivers and estuaries in Port Philip Bay, Victoria, Australia. In total, 19 PFAS were screened in grab samples of water using a combination of solid phase extraction and liquid chromatography - mass spectrometry measurement techniques. Eighteen of the PFAS screened were observed in samples. The highest level of PFOS observed at a freshwater site was 0.045 μg/L; this concentration is approximately half the draft Australian 95% species protection level for total PFOS. The highest level of PFOA in the study (0.014 μg/L) was some four orders of magnitude lower than the draft Australian trigger value for PFOA (220 μg/L). However, none of the PFAS observed at the freshwater sites had research quotient (RQ) or toxicity unit (TU) values above 1 or -3, respectively. The highest concentration of PFOS observed at an estuarine site was 0.075 μg/L; the highest level of PFOA, 0.09 μg/L). There are no Australian marine water quality trigger values for PFAS, so potential risk was assessed using the European environment quality standards (EQS) adopted in EU Directive 2013/39/EU, RQ and TU methods. In that context, none of the PFAS observed at estuary sites had concentrations higher than the EU standards, or RQ above 1 or Log TU above -3. Together these assessments suggest none of the PFAS screened would have posed an acute risk to organisms in the fresh or estuary waters studied at the time of sampling on an individual or collective basis. However, the detection of these PFAS in Victorian estuaries highlights that the issue is not just an issue for more densely populated countries in the northern hemisphere, but also potentially of concern in Australia. And, in that context, more sampling campaigns in Port Philip Bay are of paramount importance to assess the potential risk pose by these compounds to aquatic ecosystems.