Trifluoroacetic acid (TFA), an emerging ultra-short-chain perfluoroalkyl acid (PFAS) characterized by extreme persistence and mobility, globally accumulates in marine environments as its primary geochemical sink. In this study, a liquid-liquid extraction followed by gas chromatography-mass spectrometry derivatization (LLE-GC-MS) method was applied to determine TFA concentrations in surface seawater and along vertical profiles in the Beibu Gulf, a typical semi-enclosed bay, during both winter and summer campaigns. Preliminary evaluation indicates spatial heterogeneity and potential seasonal variations of TFA within the gulf. Integrated with the regional physical oceanographic framework, this study explores the potential influences of localized hydrodynamic processes—such as coastal circulations and water mass mixing—on the spatial allocation of highly water-soluble emerging contaminants. Given the strong hydrological conservatism of TFA in aqueous systems, its spatial distribution profiles provide subtle insights into complex transport mechanisms in margin seas, highlighting its potential utility as a geochemical tracer for oceanic dynamic processes.