The physico-chemical changes may have the tendency to accumulate in the various organs of estuarine organisms, especially fish which may in turn enter into the human metabolism through consumption causing serious hazards. Hence, the present study was carried out to determine the physico-chemical characteristics of water and Ichthyofauna in Arasalar estuary in southeast coast of India for the period of 1 year during September 2012-August 2013. The environmental parameters such as, temperature, pH, salinity, DO, silicate, nitrate and phosphate were observed from Department of Zoology, Rajah Serfoji Goverment College, Thanjavur, Tamil Nadu, India. During the period of study, air temperature varied from 28.8 to 35 degrees C. The surface water temperature also varied from 25 to 31.5 degrees C. The monthly mean values of hydrogen ion concentration of water varied from 7.1 to 8.2. The salinity of water varied from 5.5 parts per thousand to 34. Dissolved oxygen in Arasalar estuary was varied from 3.5 to 7.2 mg/l. The total phosphorus varied from 0.29 to 2.15 mu g/l. The nitrate varied from 0.47 to 3.75 mu g/l. The silicate content varied from 28.25 to 98.74 mu g/l. Totally 866 fishes were collected belonging to 4 orders and 5 families. Mystus gulio was found to be the dominant species (25.40 %) in the study area.