The occurrence and fate of polyfluoroalkyl compounds (PFCs) in the aquatic environment has been recognized as one of the emerging issues in environmental chemistry. PFCs comprise a diverse group of chemicals that are widely used as processing additives during fluoropolymer production and as surfactants in consumer applications for over 50 years. PFCs are known to be persistent, bioaccumulative and have possible adverse effects on humans and wildlife. As a result, perfluorooctane sulfonate (PFOS) has been added to the persistent organic pollutants (POPs) list of the Stockholm Convention in May 2009. However, their homologues, neutral precursor compounds and new PFCs classes continue to be produced. In general, several PFCs from different classes have been detected ubiquitously in the aqueous environment while the concentrations usually range between pg and ng per litre for individual compounds. Sources of PFCs into the aqueous environment are both point sources (e.g., wastewater treatment plant effluents) and nonpoint sources (e.g., surface runoff). The detected congener composition in environmental samples depends on their physicochemical characteristics and may provide information to their sources and transport pathways. However, the dominant transport pathways of individual PFCs to remote regions have not been conclusively characterised to date. The objective of this article is to give an overview on existing knowledge of the occurrence, fate and processes of PFCs in the aquatic environment. Finally, this article identifies knowledge gaps, presents conclusions and recommendations for future work.