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Globally, there is growing concern over the environmental contamination of coastal ecosystems caused by anthropogenic activities. Here,we performed a study to evaluate the degree of heavy metal contamination in 5 different sediment samples collected from five sites along the Southeastern coast of India. Additionally, the research aims to explore the potential ecological implications of heavy metal contamination on the bacterial diversity, a crucial factor in upholding a sustainable ecosystem. A total of  seven heavy metals, i.e., chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), mercury (Hg), cadmium (Cd) and arsenic (As), were assessed and quantified using inductively coupled plasma mass spectrometry. Targeted amplicon sequencing revealed that phylum Proteobacteria (36.9%) was the most dominating followed by Halobacterota (25.5%), Actinobacteriota (15%), Firmicutes (6.7%), Bacteroidota (4.0%), Thermoplasmatota (2.3%), Acidobacteriota (2.0%), Chloroflexi (1.6%), Planctomycetota (1.2%) and Crenarchaeota (1.1%). According to the alpha diversity estimate, lesser bacterial diversity was observed in areas with high pollution levels. Moreover, the physicochemical parameters of the sediments were analyzed. The contamination levels of the sediments were evaluated using the geo-accumulation index (Igeo), contamination factor (CF) and pollution loading index (PLI) to ascertain the comprehensive toxicity status of the sediments. The Igeo values revealed sediment pollution with metals such as Hg and Cd. The sediments obtained from the sampling site PU-01 showed the highest concentration of Hg pollution. Considering the ecotoxicological aspect, the estimated risk index (RI) values indicated a range from low to significant ecological risk., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)