Coastal sediments play a dual role in biogeochemical processes, both as a medium for substance storage and transformation, and as a natural archive, recording the historical traces of environmental change, including possible change of mangrove coverage and species composition. This study is to disclose the mangrove zone in modifying the biogeochemical characteristics of sediments. The 50 cm sediment cores were collected at three stations representing variations in mangrove and non-mangrove stand structure and analyzed in various layers. Grain size, color, pH, salinity, oxidation-reduction potential (ORP), organic carbon (C-organic), total nitrogen (TN), ammonium (NH4+), nitrite (NO2-), nitrate (NO3-), phosphate (PO43-), and total phosphorus (TP) were measured from concerned layers of sediments. The results revealed that gradual decreases in pH, ORP, C-organic, and nutrient concentrations in mangrove sediments profiles were observed, suggesting chemical processes associated with increasing anoxic/reducing conditions in deeper layers. In contrast, those in the non-mangrove sediments apparently varied. Principal component analysis (PCA) demonstrated clear spatial segregation among stations. Mangrove sediments were characterized by fine-grained sediments, higher C-organic, and enriched nutrient profiles, whereas coarser textures, alkaline conditions, and low nutrient concentrations were observed in the non-mangrove sediments. Different profiles of sediment properties across these distinctive zones were also identified. These weaker associations with any dominant parameter were probably related to the influence of sparse stand structure, simple mangrove morphology, and dynamics of site hydrology. These findings highlight the critical role of mangrove in biogeochemical processes to form and modify properties of the physico-chemical sediment, and possibly the ecological function of coastal environments.