The response of macrobenthic communities to both environmental and anthropogenic pressures serves as a valuable indicator of ecosystem integrity. This study aimed to unravel the benthic community structure, examine the heavy metal contamination status, and explore the response of the microbenthic community to heavy metals in a tropical shipbreaking region. For this, sediment and benthos samples were taken from different sampling stations of the shipbreaking area and the non-shipbreaking sites. The results showed the benthic community consisted of 23 taxa, including Polychaeta, Oligochaeta, Amphipoda, Decapoda, Gastropoda, Bivalvia, and Priapulida, with polychaetes being the predominant group. The benthic community and diversity values were significantly varied between the two sampling sites (p <0.05). Taxa richness was lower in the shipbreaking area, primarily characterized by the dominance of opportunistic benthic groups, particularly Capitella sp. The concentrations of heavy metals (µg. g−1) in the sediment varied within the following ranges: 35.54–258.021 for Zn, 4.84–132.08 for Pb, 22.82–75.25 for Cu, 198.74–764.16 for Mn, 14.57–42.13 for Cr, 4.03–42.23 for Ni, and 3.82–14.85 for Co. Based on concentration levels, Zn, Pb, and Cu were identified as major contaminants with moderate to high potential for adverse effects, particularly evident in the shipbreaking area compared to non-shipbreaking areas. Pollution indices, including enrichment factors and contamination factors, also highlighted contamination by Zn, Pb, and Cu. Among the benthic taxa, Polychaeta demonstrated a high degree of tolerance to elevated concentrations of these heavy metals. Amphipoda density was significantly negatively correlated with Zn, Pb, and Cu concentrations, with significant coefficients of determination (r2= 0.38, p <0.10; r2= 0.64, p <0.01 and r2 = 0.63, p <0.01, respectively). Multivariate analyses (cluster analyses, MDS and CCA) demonstrated both positive and negative relationships among heavy metals and benthic groups. Canonical Correspondence Analysis (CCA) showed the benthic community was negatively correlated with Zn, Pb, and Cu. This finding provided critical insights into the ecological health of aquatic ecosystems, aiding in the development of informed conservation and management strategies.