Interrelation between plankton groups and water chemistry variables in two lakes of Mysore (Hadhinaru lake and Arasanakere lake).were studied. Multivariable analysis was used for the study; Canonical Correspondence Analysis indicated that in Hadhinaru lake Desmids and Euglenaceae were negatively correlated to physico-chemical parameters and in Arasanakere lake very few plankton showed +ve correlations. Desmids showed high correlation with physico-chemical variables correlation coefficient were significantly high in both water bodies CCA serves as an important tool in freshwater ecological studies.