Algae as indicators of organic pollution in 20 lakes of southern Karnataka have been studied. The Palmer's algal index of organic pollution has been discussed. The IDSE/5 Diatom index is calculated using the OMNIDA software. The order of tolerance to organic pollution was calculated using the Garrett ranking technique. Nestedness of species in the lakes was also determined using the Nestedness calculator. According to the Palmer's index all the 20 lakes are organically polluted. Bogadi Lake was least while Dadadahalli Lake and Karanji Lake were heavily polluted. The present work compares the use of old and new techniques of detecting water quality. It also enables to understand weather algae can be of importance in conserving organically polluted lake waters. The nestedness analysis helps in detecting the autocathonous algae in each lake in contributing to organic pollution. The species index indicated that Doddakere Lake, Kabini Lake, Kalale lake, Kurubara lake, Hadhinaru Lake and Bogadi lake had low organic pollution. The diatom index showed that all lakes ranged between moderate and high organic pollution, but the degradation levels in the water were always high. Dadadahalli Lake has the highest organic pollution while Kalale Lake and Makanahally Lake were heavily polluted. Species of Euglena and Scenedesmus were the most tolerant species. Algae were highly nested in Dadadahalli Lake, Dalvoi Lake, Karanji Lake and were the most hospitable sites for growth of algae while most of the other lakes had idiosyncratic species. The matrix fill was low (59.5%) and the system temperature was warm (34.22o) indicating poor distribution of algal species. The use of modern tools in determining levels of organic pollution in lake ecosystems has been discussed.