The transport of trace metals from the land to ocean has a number of different routes and efficiencies. The sources of toxic elements into the rivers to be debouched into the sea through estuaries are either weathered naturally from the soils and rocks or introduced anthropogenically from point or non-point sources, in labile form or in particulate form. However, recent studies indicate that the transport of trace elements to the aquatic environment is much more complex than what has been thought. The chemistry and ecology of an estuarine system are entirely different from the fluvial as well as the marine system. Estuarine environment is characterized by a constantly changing mixture of salt and freshwater. In the present study area Manakudy estuary is situated about 8 kilometres north west of Kanyakumari (Latitude N 08° 05´ 21.8´´and Longitude E 077° 29´ 03.7´´). To gain a better understanding of the geochemical behavior of physico-chemical parameters and trace elements in the estuary and to examine variations in associated chemical fluxes, 20 water samples were collected throughout the Manakudy estuary, a minor river in south-western India.