Heavy metal contamination has threatened India’s biodiverse-rich coastal wetlands, backwaters, rivers, estuaries and mangroves due to unscientific industrial activities and urbanisation. Among the Indian states, the Cochin city is the commercial and economic hub of Kerala along the coastal belt of Arabian Sea. Mangroves located are on the backwater channels and along the banks of Cochin estuary are near victims of this commercialization. Therefore, a comprehensive analysis of the sediment quality focusing on heavy metal contamination and pollution problems are documented from the mangrove habitats of Cochin, considering their immense ecological services offered to the coastal communities with an insight for future restoration activities. Out of the 17 metals analysed, concentration of 6, largely exceeded NOAA effect range low (Cr (5.5–202), Cu (0.89–40.68), Cd (0–1.34), Hg (0–0.68)) and effect range medium (Ag (0–4.68), Ni (0.06–64.5)), which marks the probability of adverse biological effects on mangrove plants and animals. Enrichment factor analysis revealed extremely severe enrichment of Ag (EF = 133), Hg (18.8), Pb (17.8) and Cd (17) and was supported by PCA analysis, that clearly derived the anthropogenic influence of Ag, Cd and Hg in mangroves. Contamination factor, geoaccumulation index and pollution load index revealed that the mangrove sites of Cochin are nearly stressed due to contamination (CF = 66.8) and extreme pollution effects ( I geo  = − 1.8–5.4) due to silver, and considerably contaminated (CF = 4.4) with Cd especially in Aroor and Vypin zones. However, Valanthakad zone was almost free from metal pollution having better sediment quality where mangrove vegetation had luxuriant growth.