In the present study, efforts have been made to analyze selected physico-chemical characteristics of the water bodies of Uppanar estuary and Periyavaikkal region of Killai backwater area, Cuddalore District, Tamilnadu India. The comparative analytical study was conducted for one calendar year and water samplings were done on monthly basis. The parameters analyzed include rainfall, atmospheric temperature, water temperature, pH, salinity, turbidity, total dissolved solids, electrical conductivity, dissolved oxygen, biochemical oxygen demand and hardness. The results of the study clearly indicate the environmentally degraded ambience of Uppanar estuary and a comparatively less polluted water body at Killai region. The study also indicated significant seasonal variations among the parameters within each sites as well as between sites indicating the eco-toxicological susceptibility of Uppanar estuary.