Diatoms in particular are of utmost importance, as potential indicators of water quality due to their sensitivity and strong response to many physical, chemical and biological changes. As a major contributor to primary productivity in the aquatic ecosystem, diatoms play a pivotal role in the food chain. Due to their ubiquitous nature, they are abundantly present in aquatic environments. This paper presents data on the water quality assessment using diatoms in Thonnur and Sulekere lakes of Mandya district, Karnataka, India. Organic as well as anthropogenic pollution indicators were found in both the lakes. Anthropogenic pollution was high in case of Thonnur lake compared to Sulekere lake. Indicators of organic pollution comprised of Nitzschia palea, Gomphonema parvalum and Nitzschia fragalis. Indicators of Anthropogenic pollution were found to be Synedra acus and S. ulna whereas S.ulna was found to be common in all sites of both the lakes because of high anthropogenic activity. About 10-12 species were identified in sulekere lake and 5-6 species in thonnur lake were recorded. Hence, diatoms play an imperative key role in water quality monitoring and also they are important resource for identifying ecological condition of the lake. So our findings highlighted that Sulerkere lake is more polluted than Thonnur lake. Worsening of water quality in both the lakes was due to human activities and organic pollution.