Background The concentration of heavy metals and their spatial distribution in surface sediments collected from the Thondi coast, Palk Bay, South India were analysed in this study. The sediment grain size, pH, EC, and heavy metal concentrations (Mn, Fe, Cr, Zn, Cd, Ni, Cu, and Pb) were determined and the values for the geoaccumulation index (Igeo), enrichment factor (EF), potential contamination index (Cp), potential ecological risk index (PERI), contamination factor (CF), modified contamination degree (mCd), degree of contamination (Cd), and potential contamination factors (Cp) were calculated based on their background values to determine the pollution level of the study area. The sediment grain size, pH, EC, and heavy metal concentrations were determined and the values for the pollution indices were calculated based on their background values to determine the pollution level. Results The pollution indices, namely EF, CF, Cd, mCd, CP, \({\text{E}}_{\text{r}}^{\text{i}}\), and PERI, except for Igeo, revealed that the heavy metal contamination was due to Cd, while a moderate level of contamination was caused by Cu, Zn, Pb, and Cr. The principal component analysis and correlation matrix analysis showed a strong positive loading for Cd due to its high level of contamination in the study area. Anthropogenic inputs such as municipal wastewater, domestic sewage discharge, fishing harbour activities, and industrial and aquaculture wastes led to the increased Cd concentration in the study area. Moreover, the pollution load index revealed that the sediments were polluted by heavy metals. Conclusion The findings of this study revealed that the increased concentration of heavy metals in the study area increases the toxicity in the marine environment, thus affecting the ecosystem.