This study investigates the presence, distribution, and potential impacts of perfluoroalkyl substances (PFASs) and hexabromocyclododecanes (HBCDs) on the Antarctic marine environment. The analysis results from the King Sejong Station, the Jang Bogo Station, and Cape Evans revealed the highest concentrations of both PFASs and HBCDs at King Sejong Station, indicating the significant influence of human activity. Short-chain perfluorocarboxylic acids (PFCAs) dominated the seawater samples, with PFPeA at the highest concentration (0.076 ng/L) at King Sejong Station, whereas perfluorosulfonic acids (PFSAs) were prevalent in the sediments, with PFHxS reaching 0.985 ng/g. Total PFASs in benthos ranged from N.D. to 2.40 ng/g ww across all stations. This indicated the effects of long-range transport and glacial meltwater. α-HBCD was the most common diastereomer in benthos samples, detected in 58.3% of samples, suggesting its selective persistency. Although risk quotient analysis revealed low immediate risks to lower-trophic organisms, potential risks remain owing to their persistence and bioaccumulation potential. Contaminant patterns changed after regulations: perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) levels decreased, unregulated PFASs increased, HBCD stereoisomer ratios shifted towards α-HBCD dominance, and overall HBCD concentrations declined. Widespread persistence of regulated substances was observed in Antarctic environments, highlighting the need for comprehensive and long-term monitoring strategies. This study provides essential baseline data on contaminant distributions across the Southern Ocean, contributing to our understanding of emerging pollutants in Antarctic regions and informing future environmental protection efforts.