Organotin compounds (butyl-, phenyl-, octyl- and tributylmonomethyltin) and inorganic tin were quantified in sea-water and sediments from two harbours and several locations on the southeast coast of India using highly sensitive and selective gas chromatography-inductively coupled plasma mass spectrometry (GC-ICP-MS), adopting new extraction and analytical techniques with extremely low detection limits (water, 0.019–0.85 pg l⁻¹; sediment, 0.23–0.48 ng g⁻¹). The concentrations of monobutyltin (MBT), dibutyltin (DBT) and tributyltin (TBT) in sea-water from Tuticorin harbour varied from 0.64 to 4.97, 3.0 to 26.8 and 0.3 to 30.4 ng Sn l⁻¹, respectively. MBT, DBT and TBT in sediments from harbour areas ranged from 1.6 to 393, 1.3 to 394 and ND (not detected) to 1280 ng Sn g⁻¹ (dry weight), respectively. Natural methylation in both harbours was established by quantifying tributylmonomethyltin (TBMMT) residues (sea-water, ND–0.19 ng Sn l⁻¹; sediment, ND–765 ng Sn g⁻¹ dry weight). In sea-water, octyltins were also determined as monooctyltin (MOT) > dioctyltin (DOT) > trioctyltin (TOT). Butyltin contamination in commercial harbours is evident, but other coastal waters are not contaminated with organotin residues. The high concentration of inorganic tin in estuarine sediment indicates an elevated rate of debutylation in the estuarine environment. Both methylation and debutylation of TBT in Chennai harbour were greater than in Tuticorin harbour. A significant correlation (r² = 0.75) between total butyltin and organic carbon contents in sediment was found. To our knowledge, this is the first report on the distribution of butyltins and methylated butyltin in sea-water and sediment and octyltins in sea-water in the Indian marine environment.