Phytoplankton communities are widely used to assess the present conditions about eutrophication status, and physical and chemical parameters of aquatic environment. Therefore, phytoplankton communities are named as bio-monitoring agent. The assessment of phytoplankton density provides a cost-efficient method to analyze eutrophication conditions in both fresh and marine water ecosystems. Hence, the present research was focused on the phytoplankton diversity in two perennial lakes of Coimbatore city, and they correlated with Palmer index to get knowledge about polluted conditions of lake water. Results from the study revealed, totally 36 species of phytoplankton were recorded under 23 genera, which includes 14 species of Cyanophyceae, 10 species of Chlorophyceae, 09 species of Bacillariophyceae and 03 species of Euglenophyceae. Phytoplankton density was dominated by the following order Cyanophyceae ˃ Chlorophyceae ˃ Bacillariophyceae ˃ Euglenophyceae in two perennial lakes. Among these four major groups, Cyanophyceae and Chlorophyceae were abundantly found in two perennial lakes, and they are highly dynamic and bloom producing phytoplankton groups, which impair the basic use of surface water in aquatic ecosystems. They correlated with pollution indices by Palmer (1969) [34]. The two perennial lakes are impacted by various pollutions caused by pollutants such as agricultural wastes, municipal wastes, and industrial wastes are influence the density of phytoplankton communities and hydrographical profile of lake water. Therefore, continuous monitoring of two perennial lakes is very necessary for primary production and wetland ecosystems in Coimbatore district.