Marine ecosystem is being threatened by the discharge of untreated sewage wastes and industrial effluents which ultimately affects the sustainability of living resources and public health. These wastes carry enormous level of toxicants especially the heavy metals have the tendency to accumulate into the basic food chain and move up through the higher trophic level and results in negative impact on the marine resources thus causing economic loss. In this regard, to ascertain the level of heavy metals in water, particulate, zooplankton (Zn, Mn, Pb, Cu, Cd and Hg) and in sediment (Pb, Al, Cd and Hg) along southern Kerala coast, India has been evaluated during early 2006. The heavy metal concentrations followed the hierarchy; Zn>Mn>Pb>Cu>Cd>Hg; Pb>Zn>Mn>Cu>Cd>Hg; Zn>Pb>Mn>Cu>Cd>Hg and Pb>Al>Cd>Hg in seawater, particulate matter, zooplankton and sediment respectively. The results revealed that in all the transacts (except Cochin) the heavy metal concentrations are below the threshold levels associated with the toxicological effects and the regulatory limits. Metal enrichments were observed close to the major urban areas of coastal waters, mostly associated with large scale industrialization. Enrichment factor, geoaccumulation index and pollution load index were calculated to evaluate the heavy metal threats along the coastal sediment. It revealed minor to moderately severe enrichment of Cd, Pb and Hg in the industrial zones of the coastal stretches especially at Cochin. A comparison with sediment quality guideline quotient indicated that there may be probability of ecotoxicological threats to the benthic community along Cochin transect.