Due to non-scientific industrial activity and urbanization, trace elements contamination has posed a threat to Malaysia's biodiversity-rich coastal wetlands, streams, estuaries, and mangroves. Commercialization has taken a toll on mangroves in backwater canals and along the banks of the Sepang River. As a result, a thorough examination of sediment quality from the Sepang River mangrove habitats is done with a focus on trace element pollution and pollution issues, taking into account the enormous ecological services that are offered to coastal communities and offering guidance for upcoming restoration efforts. The concentration of trace elements (Cr, As, Pb, Ni, Mo, Co, Cd, and Hg) in the sediment samples was measured using an induced plasma mass spectrometric (ICP-MS). Results of the study revealed that Arsenic (As) levels exceeded the Canadian range of low effects, indicating the possibility of deleterious biological consequences on mangrove plants and animals. In all sampling locations, the enrichment factor (EF) analysis revealed extraordinarily high enrichment of As (9.89–23.65) and Mo (4.74–12.03). The geo-accumulation index of As (1.83 – 3.04), Mo (1.40 – 2.74), and Cd (0.652 – 3.03) revealed that mangrove locations in the Sepang River have almost extreme pollution effects. Pearson's correlation, which deduced the anthropogenic influence of As, Cd, and Mo in mangroves, backed up this claim. Results of the study recommended that continue monitoring of pollutants released from anthropogenic sources is highly required and there is a strong need to take more stringent measures to protect the environment.