Mangrove ecosystems provide various ecosystem services. However, its existence is increasingly threatened by human activities that disrupt its functions. Significant mangrove loss has been documented on the north coast of Java Island, Indonesia, particularly in Pasar Banggi Village, Rembang, Indonesia. Although this area is included in an essential ecosystem area (EEA) that designated as a protected area, Pasar Banggi Village still faces anthropogenic threats from its surrounding environment. Therefore, the ecosystem function of this mangrove area requires further study to ensure the EEA has a significant impact on protection and restoration efforts. One of the studies discussed is the capacity of the remaining mangroves to sequester trace metals has not been thoroughly assessed. This study evaluated the contamination levels, trace metal load-bearing capacity, and physicochemical factors influencing mangrove sediments in Pasar Banggi Village. Sediment samples (n = 9) were collected from three depths—surface (0–10 cm), intermediate (10–20 cm), and deep (20–30 cm) —at three representative monitoring stations (ST 1, ST 2, and ST 3). Sediment sample digestion was conducted using the USEPA 3050B method, and trace metal concentrations were measured via inductively coupled plasma mass spectrometry (ICP-MS), along with key environmental variables (total carbon (%C), salinity, soil pH, and temperature). To evaluate contamination levels, potential origins, and the connections between parameters and locations, data interpretation utilized the enrichment factor (EF), geo-accumulation index (I-geo), and Principal Component Analysis (PCA). Results indicated mean trace-metal concentrations in the order of Fe > Mn > Zn > Cu > Pb > As. Generally, EF values suggested negligible enrichment, although moderate enrichment was noted for As, Cu, and Zn at specific depths, while I-geo values categorized all parameters as “unpolluted.” However, the PCA biplot revealed significant spatial and depth-related variation. Component 1 captured heavy metal variance (As, Fe, Mn, Zn, Cu, Cd, and Pb), identifying Station 3 (particularly its surface layer) as a localized multimetal accumulation hotspot, where concentrations decreased with depth. In contrast, component 2 was influenced by localized soil properties. Station 2 strongly clustered with high organic carbon (%C), salinity, and alkaline pH across all depths, and showed a negative correlation with heavy metals. Station 1 served as a pristine baseline reference site with low contaminant loads and organic inputs. The findings suggest a notable human-induced variation among specific areas with concentrated metal presence, and natural soil variables imply distinct environmental sources and transport mechanisms that affect the ecological landscape.