Mercury and arsenic are the toxic heavy metals found in water, sediment and in different species of fish tissue, Rastrelliger kanagurta(Indian Mackerel), Nemipterus spp., (threadfin beam), Parapenaeopsis Maxillipedo (shrimp), Metapenaeus dobsoni (shrimp), Perna sp. (bivalve), Sepia sp.(Cephalopod-cuttlefish) and Loligo sp.(Cephalopod–squid) of the Chennai, Ennore estuary. The water, sediment and fish tissues were analysed for mercury and arsenic using standard procedure in Atomic Absorption Spectrophotometry. The maximum mercury concentration in water is 0.02ppb±0.01, in sediment is 0.30 ppb±0.01 and in different fish tissue species in Rastrelliger Kanagurta, 0.25ppb±0.06, Nemipterus spp., 0.54ppb±0.06, Parapenaeopsis Maxilli - pedo 0.58ppb±0.06, Metapenaeus dobsoni, 0.34 ppb±0.06, Perna sp., 0.61ppb±0.06 and Sepia sp. 0.72ppb±0.06 and Loligo sp.,Cephalopod-squid, 0.38 ppb±0.06 in the first quarter. Among the fish species selected for the study during Apr-June’09, the lowest mercury content is in Rastrelliger kanagurta (Indian Mackerel), 0.35ppb±0.11 followed by Metapenaeus dobsoni,0.68ppb±0.11, Sepia spp., 0.76ppb±0.11, Loligo sp. (Cephalopod squid), 0.78 ppb±0.11 and Nemipterus spp. (threadfin bream), 1.29ppb±0.11 during second quarter. The percentage increase in mercury during first quarter is 64.67% from lowest to highest. The percentage increase in mercury during second quarter is 55.99% from lowest to highest. The percentage increase in mercury content in µg/g (ppb) was 80.27% from lowest to highest. The metal concentration in tissues µg/g (ppb) ranged between 0.26-1.29µg/g (ppb) in mercury. Among the fish species selected for study for arsenic during JanMar’09, the lowest arsenic content is in Rastrelliger Kanagurta (Indian Mack erel), 3.85ppb±8.22 followed by Nemipterus spp. (threadfin bream), 6.10ppb±8.22, Loligo sp., 26.09ppb±8.22, Metapenaeopsis Maxillipedo (shrimp), 34.72 ppb±8.22, Parapenaeopsis Maxi - millipedo (shrimp), 43.84ppb±8.22, Sepia spp., 52.09ppb±8.22 and Perna sp. (bivalve) 60.13 ppb±8.22 in the first quarter. Among the fish species selected for the study during Apr-June’09, the lowest arsenic content is in Rastrelliger kanagurta (Indrai Mackerel), 4.35ppb±7.88 followed by Nemipterus spp. (threadfin bream), 13.12ppb±7.88, Metapenaeus dobsoni (shrimp) 14.92 ppb± 7.88, Sepia sp., (Cephalopod cuttlefish), 18.74ppb±7.88 and Loligo sp. (Cephalopod –squid) 45.09 ppb±7.88 in the second quarter. The percentage increase in arsenic during first quarter is 93.58%. The percentage increase in arsenic during second quarter is 90.34%. The percentage increase in arsenic content value in µg/g(ppb) was 93.58%. The metal concentration in tissues, µg/g (ppb) ranged between 3.85-60.13µg/g(ppb). The lowest mercury in tissue was found in the species Rastrelliger Kanagurta was 0.25µg/g (ppb)±0.06 and in arsenic it was 3.85µg/g, (ppb) ±8.22 the highest mercury in tissue was found in the Nemipterus sp., 1.29µg/g(ppb)±0.11, the highest arsenic was found in 60.13µg/g (ppb)±7.88 in Perna sp.(bivalve).