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Mangrove sediments are strong modulators of organic matter (OM) content and pollutant dynamics, acting both as sinks and sources of these components. This study aimed to assess temporal dynamics of OM within temperate mangrove sediments and their ability to sequester pollutants. Specifically, levels of trace metals (Fe, Cu, Zn, Pb, Cd) and a metalloid (As) were examined within mangrove and mudflat sediments located in a high-energy environment in Mangawhai Harbour Estuary, northern New Zealand. Sediment cores were collected from a mangrove stand and adjacent mudflats at three sediment depths during different months over a year. Variations in OM and elements were compared to rainfall and temperature patterns observed during the sampling period. All element concentrations, except for those of As, were significantly higher in mangrove compared to mudflat sediments during the entire sampling period. This is consistent with the well-reported ability of mangroves to trap suspended particles and OM. In addition, we observed a decreasing trend in trace metal concentrations with increasing sediment depth within mangrove habitat, which correlated well with decreasing OM content. Our results also suggested that most elements had different, but significant, temporal variations throughout the year, especially in mangrove sediments. Overall, the concentrations of Cu, Zn, Pb, Cd, and As in mangrove sediments increased during summer, whereas maximum levels of Fe and OM were observed in winter. This temporal pattern was determined to be related to OM and redox cycling as a result of changes in effluent input rates and physical/chemical environments during different seasons.