Abstract: To assess the pollution status of emerging contaminants (ECs) in the mangrove wetlands of Shenzhen, this research conducted a sampling survey on the ECs across all mangrove wetlands in the city, and assessed the pollution risks through bioaccumulation effect and risk quotient analysis. The results showed that the concentrations of per- and polyfluoroalkyl substances (PFAS) and antibiotics in the western mangroves of Shenzhen were generally higher than those in the eastern ones. The concentration of PFAS in seawater during the dry season was about 2.5 times higher than that during the wet season, and the concentration of short-chain PFAS was generally higher. Among them, the concentration of sulfadiazine and lincomycin in the seawater and sediment of the Neilingding Reserve was the highest. Among the endocrine disrupting chemicals (EDCs), 4-nonylphenol (4-NP) had the highest concentration (49.10 ng/L) in the Maozhou River, and bisphenol A (BPA) in the sediment of Futian was prominent (11.80 ng/g, dry weight). Bioaccumulation assessments indicated that the bioaccumulation effect of antibiotics was most significant in the Xibay mangrove, and BPA was among the major bioaccumulative EDCs. Ecological risk assessment revealed that perfluorobutyric acid had a strong bioaccumulation capacity, and the bioconcentration factor (BCF) values of sulfonamide antibiotics at points such as Baguang and Xichong far exceeded 5000 L/kg. Furthermore, the risk quotient (RQ) of 4-NP exceeded 0.1 at five sites, indicating a medium-level ecological risk. This study elucidated the spatial heterogeneity and bioaccumulation characteristics of ECs across environmental matrices, highlighting the necessity of implementing source control, enhanced ecosystem restoration and functional enhancement, and long-term monitoring to mitigate EC-related ecological risks.