Monitoring of water quality with regards to physical and chemical properties and distribution of nutrients are inadequate. Biological indicators of water quality monitoring developed during the recent years have served an excellent tools in the area of water pollution studies. According to the Western Australian Planning Commission (2003) water protection integrated over time and space has become a high priority issue for the public and government at all levels. Among all the algae, fresh water diatoms are the most commonly used indicators of the conditions of the water. Several diatom indices are tested for lakes in other countries, but have not used for river water systems. Diatom monitoring studies in India have suffered since their identification is difficult and extensive literature is not available mainly. Therefore the study aims that identification of diatom flora and distribution of nutrients in fresh water river in Chidambaram. Water samples from palaman river were collected during January 2011 to December 2011 at monthly intervals for studying various physico-chemical parameters and nutrient were analysed viz. Temperature, pH, Salinity, Dissolved oxygen, Biological oxygen demand, Chloride, Phosphate, Sulphate, Nitrate, and Silicate. Phytoplankton density and diversity was more or less uniform throughout the study period. However the community structure of the phytoplankton varied from season to season. During post-monsoon and summer 15 genera of the phytoplankton were recorded whereas 9 genera were recorded during pre-monsoon season. Nitzschia intermedia, Cyclotella meneghiniana, Cyclotella automus, Navicula cryptocephala, Melosira varians were strong indicators of organic pollution, while Amphora ovalis, Pinnularia gibba, Synedra ulna, Synedra acus, Cymbella tumida, Gomphonema olivaceum, Nitzchia gracilis, Cocconeis pediculus and Navicula amphiceropsis were indicators of anthropogenic pollution which was mainly due to cattle ranching around these river. Possible causes for the temporal variation of the water quality parameters and community structure of the phytoplankton have been described.