Associations of legacy and emerging per- and polyfluoroalkyl substances (PFAS) with aquatic communities in a typical subtropical estuary

• PFAS substitutes contributed more to total concentrations in a subtropical estuary. • F-53B, a PFOS substitute, showed a significant trophic magnification effect (p < 0.05). • The environmental impacts of PFAS were extended to the aquatic community level. • Increasing PFAS concentrations were significantly negatively correlated with fish diversity. Coastal estuarine ecosystems play a critical role in supporting biodiversity but are increasingly threatened by per- and polyfluoroalkyl substances (PFAS). This study combined in situ PFAS monitoring with environmental DNA (eDNA) metabarcoding to investigate their impacts on fish species and community structure. PFAS concentrations ranged from 7.34-82.04 ng L −1 in water and 1.87–4.98 ng g −1 dw in sediments. Perfluorobutanoic acid (PFBA) and perfluorobutane sulfonic acid (PFBS) replaced perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) as the predominant PFAS in water, with mean concentrations of 3.74 ± 2.67 ng L −1 and 13.84 ± 3.95 ng L −1 , respectively. In organisms, PFAS concentrations ranged from 0.13 to 96.21 ng g −1 ww and were higher in benthic invertebrates. As alternatives to PFOA and PFOS, PFBA and PFBS displayed comparable or even greater bioaccumulation potential, whereas chlorinated polyfluoroalkyl ether sulfonic acids (F-53B) exhibited significant trophic magnification (p < 0.05). PFAS occurrence was closely associated with fish community diversity, and increasing PFAS concentrations were linked to a potential decline in the Shannon index (p < 0.05). From a species-community perspective, typical PFAS in estuarine environments exhibit bioaccumulation and trophic magnification, underscoring the need for further attention to their ecological impacts at both species and community levels.