The present study revealed the diversity of microalgae and cyanobacteria in the fresh water samples from of Thanjavur, Karaikudi and Tiruchirappalli locations, Tamil Nadu, India. A total of 94 species microalgae belonging to three taxonomic groups were identified, of which 47 species were belonging to Cyanophyceae, 16 species from Chlorophyceae and 37 species from Bacillariophyceae. Oscillatoria sp., Nostoc sp., Microcystis sp., Chroococcus sp., Gloecapsa sp., Merismopedia sp., Lyngbya sp. and Anabaena sp. (5%) were found to be among the cyanophyceaen family. Whereas, Bacillariophyceae, Navicula sp., Cymbella sp., Gomphonema sp., Nitzschia sp. Cyclotella sp. Gyrosigma sp. and Grammatophora sp. were predominant and in Chlorophyceae, Cosmarium sp., Chlorella sp. Ankistrodesmus sp. Closterium sp. and Selanastrum sp was found to be abundant. The environmental variables appear to play a significant role in determining the species richness and diversity.