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The study investigated trace metal accumulation in the sediments of three major mangrove ecosystems associated with the Ramsar sites of Kerala state, the ecological risks they pose, and the absorption, accumulation, and translocation of metals in five dominant mangrove species, as these systems are heavily impacted by anthropogenic interventions. The trace metal concentrations (mg kg -1 ) in the sediment of different mangrove habitats of Kerala ranged from 20 to 295 for Cu, 65 to 350 for Zn, 72 to 151 for Pb, 11 to 210 for Ni, 42 to 228 for Mn, 0 to 6 for Cd,124 to 565 for Cr, and 0 to 2.9 for Ag. An overall enrichment of metals was recorded in sediment, exceeding the prescribed effects range median (ERM) of consensus-based sediment quality guidelines (SQGs) for Cu and Cr concentrations at Munroe Island and Ni at Vypin, indicating a detrimental risk to biota in the sediments. Principal component analysis and a higher geoaccumulation index indicated the contribution of trace metals from industries, agricultural runoff, and urban waste disposal. The ecological risk index suggested that cadmium poses a very high risk to the mangrove ecosystem at Vypin. Furthermore, the bioconcentration factor for various trace metals in Avicennia marina and Lumnitzera racemosa in Ayiramthengu was > 2, suggesting that these species can accumulate trace metals, particularly Cr, Cd, and Pb. Further, our findings suggest that A. marina may be considered as an efficient metal trap for Cd in aerial parts, as indicated by the significant translocation factor (> 1) combined with the bioconcentration factor. Therefore, the study revealed that Munroe island and Vypin had a considerable level of contamination for toxic metals and Avicennia marina could be a promising candidate species for the phytoremediation of these trace metals in the coastal settings of Kerala state., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)