Purpose: Coastal ecosystems such as mangroves and saltmarsh are recognized sinks for carbon (C) and support the retention of geochemical elements (GEs) and metal contaminants. The retention capacity is controlled by the GE properties, physicochemical characteristics of the soil, and the plant community. This study aims to investigate the retention, temporal variation, and contamination patterns of GEs (Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Ti, and Zn) in the soils of different coastal habitats on Ximen Island, Zhejiang, China. Methods: Soil profile samples were collected from mangrove, saltmarsh, mudflat, paddy, and mountain forest habitats in the study area. In addition to the geochemical element concentration, organic carbon content and particle size of the soil samples were analyzed. The geo-accumulation index (Igeo), the enrichment factor (EF), and the potential ecological risk index (RI) were used to quantitatively assess the contamination patterns of GEs. The Pearson correlation and principal component analyses were used to identify the factors that influence GE accumulation. Results: Mangrove and saltmarsh exhibited higher GE accumulation than other habitats. The presence of mangrove and saltmarsh vegetation creates a favorable environment for the accelerated burial of GEs towards the surface of mangrove and saltmarsh sediments. Mangrove sediment had the highest burial rate of all GEs while saltmarsh sediment was enriched in Cd, Cu, Mn, and Zn. An increase in anthropogenic activity influenced the concentrations of GEs, specifically Cd, Cr, Cu, Ni, Pb, and Zn in the mangrove, and Cd, Cu, Pb, and Zn in saltmarsh habitats. However, the level of contamination and potential environmental hazards of GEs (Cd, Cr, Cu, Ni, Pb, and Zn) was not high across tested habitats. Conclusions: Our findings imply that mangrove and saltmarsh habitats serve as an effective trap for GE accumulation, which can serve in the protection of surrounding marine environments.