This study deals with seasonal variation of heavy metals in sediments of Muthupet lagoon, Southeast coast of India from September 2011 to August 2012. The bulk sediments were association with sand, silt and clay. Geo-accumulation index (lgeo) was used to quantitatively assess the influences of heavy metal pollution. Heavy metals were determined by using Inductively Coupled Plasma Optical Emission Spectrometer (ICP-OES) and the results were compared to permissible limits of WHO/USEPA. The minimum concentration of heavy metals in all the stations were found during the post monsoon and summer seasons and the maximum concentration of heavy metals in all the stations were found during the pre-monsoon and monsoon seasons. The reason for the pollution was land drainage, irrigation through channels and municipal wastes and also the peak agricultural activities due to the release of fresh water from reservoirs. Among all the metals iron was found to be maximum in all the stations in post-monsoon and summer season followed by magnesium and manganese. Apart from these three metal, all other six metals are recorded in moderate range. The reason for the high concentration of these metals are anthropogenic activity, agriculture, aquaculture and the rivers regular in and out flow throughout the study duration in the lagoon area.