All aquatic organisms need very low quantities of trace elements. At optimum level they are beneficial and beyond that limit it causes deleterious effects to the ecosystem. The marine biosphere is known to contain high concentration of heavy metals. Estuarine sediments from the final trap for most of the heavy metals. The metals entering the system through various sources may associate with the sediment particles either by absorption gradually sinks with sediment or they may get released when mixed with marine water due to altered physico-chemical environment. Poonthura backwater which is situated in the south west coast of India (Kerala) is polluted by different means. The additional quantities of heavy metals come from agriculture, industrial and domestic wastes. Hence sediments are indicators of the quality of overlying water; five different heavy metals were tested in the sediments of Poonthura backwater for the present study. Monthly collection of sediments and analysis were carried, out for a period of one year (April-2000 to March-2001). The five metals analyzed were copper, lead, manganese, nickel and zinc. Low level of copper was observed in all the stations while comparing other metals. The seasonal variations were also noted for all the five metals and discussed. Copyright © Enviromedia. © 2008 Elsevier B.V., All rights reserved.