Per- and polyfluoroalkyl substances (PFASs), which have their origins in both industrial processes and consumer products, can be detected at all treatment stages in wastewater treatment plants (WWTPs). Quantifying the emissions of PFAS from WWTPs into the marine environment is crucial because of their potential impacts on receiving aquatic ecosystems. In this study, the levels of five PFAS were measured in both influent and effluent sewage water samples obtained from a municipal WWTP, the discharges of which flow into False Bay, on the Indian Ocean coast of Cape Town, South Africa. Additionally, seawater, sediment, and biota samples from eight sites along the False Bay coast were also analysed. Results showed high prevalence of PFAS in the different environmental matrices. Perfluorononanoic acid was most dominant in all these matrices with maximum concentration in wastewater, 10.50 ng/L; seawater, 18.76 ng/L; marine sediment, 239.65 ng/g dry weight (dw); invertebrates, 0.72–2.45 µg/g dw; seaweed, 0.36–2.01 µg/g dw. The study used the chemical fingerprint of five PFASs detected in WWTP effluents to track their dispersion across a large, previously pristine marine environment and examined how each chemical accumulated in different marine organisms. The study also demonstrates that primary and secondary wastewater treatment processes cannot fully remove such compounds. There is thus a need to improve effluent quality before its release into the environment and promote continuous monitoring focusing on the sources of PFAS, including their potential transformation products, their environmental fate and ecological risks, particularly in areas receiving effluents from WWTP.