Abstract: In the balancing of lake ecosystem macrophytes play very important role. They have capacity to improve the water quality by absorbing nutrients with their effective root system and hence as Biofilters. An attempt was made in which samples of two Potamogeton species viz. Potamogeton crispus and Potamogeton pectinatus were collected during December 2008 to April 2009 from three different sites of Upper Lake of Bhopal. The nutrients including the Phosphorus, Potassium and Sodium in the plants were analysed and found to be high. Significant correlations in Phosphorus, Potassium and Sodium levels were apparent between the tissues of two Potamogeton species which were related to their life forms and to the limnological characteristics of the lake. The objective of the study was to know comparative purification efficiency of two species of Potamogeton in wastewater treatment i.e. in reducing the nutrient content of the water. Purification of water through macrophytes is a good example of purification of water with natural means. Results indicated that both species were capable of improving water quality by reducing nutrient concentrations. But, Potamogeton crispus rather than Potamogeton pectinatus was found more potent in improving the quality of lake water.