Heavy metal pollution in marine ecosystems is an escalating environmental concern, largely driven by anthropogenic activities, and poses potential threats to ecological health and human well-being. This study embarked on a comprehensive investigation into the concentrations of heavy metals in sediment samples and evaluated their potential ecological and health risks with a focus on Eastern St. Martin’s Island (SMI), Bangladesh. Sediment samples were meticulously collected from 12 distinct sites around the island, and the concentrations of heavy metals, including Mn, Fe, Ni, Zn, Cr, Pb, and Cu, were quantified utilizing atomic absorption spectrometry (AAS). The results revealed that the average concentrations of the metals, in descending order, were Mn (269.5 ± 33.0 mg/kg), Fe (143.8 ± 21.7 mg/kg), Ni (29.6 ± 44.0 mg/kg), Zn (27.2 ± 4.34 mg/kg), Cr (8.09 ± 1.67 mg/kg), Pb (5.88 ± 0.45 mg/kg), and Cu (3.76 ± 0.60 mg/kg). Intriguingly, the concentrations of all the measured metals were found to be within permissible limits and comparatively lower than those documented in various national and international contexts. The ecological risk assessment, based on multiple sediment quality indices such as the geoaccumulation index, contamination factor, and pollution load index, indicated a moderate risk to the aquatic ecosystem but no significant adverse impact on sediment quality. Additionally, the human health risk assessment, encompassing non-carcinogenic hazard indices for different age groups, was considerably below the threshold, signifying no immediate health risk. The total carcinogenic risk was also found to be below acceptable levels. These findings underscore the current state of heavy metal pollution in Eastern St. Martin’s Island, providing valuable insights for environmental monitoring and management. While the immediate risks were not alarming, the study highlights the imperative need for sustained monitoring and the implementation of rigorous regulations to curb heavy metal pollution in order to safeguard both ecological and human health. This warrants the development of policies that are both adaptive and preemptive to ensure the sustainable utilization and conservation of marine resources.