The geochemical condition of surface sediments in a tropical estuary and adjoining shelf region is presented for their elemental interactions using statistical methods. Principal component analysis separated two clusters comprising of (i) heavy metals possessing significant correlation with texture (organic carbon, clay and silt), which belong to sediments in the shelf region and (ii) heavy metals in high concentration showing poor correlation with sediment texture, which are of estuarine origin. Co-precipitation of iron hydroxide along with scavenging of other metals could be the principal mechanism explaining the accumulation of Cd, Cu, Pb and Zn in the estuarine sediments. Discharge of industrial effluents has lead to the present level of metal contamination in the estuary. There is an associated hazard because in this state the metals released during mineralization could be available to biota. The increased anthropogenic influence in the Cochin Estuary has probably resulted in a reduction in benthic biodiversity, where pollutant-tolerant species are found to take over the vacated niche. In contrast, the coastal environment is controlled by natural oceanographic processes, where the coastal currents and stable biogenic association normalize metal deposition. The source apportionment of metals by inorganic and bio-mediated interactions helps illuminate the processes controlling their depositional trends in pristine and impacted environments.