Wetlands are areas where water is the primary factor controlling the environment, associated plant and animal life. The present study has been conducted to investigate the environmental variables of water and to make a quantitative analysis of aquatic macrophytes. Five lakes, i.e. Tamor, Beeshazar, Kingfisher, Athaieshazar and Chepang of the Chitwan National Park were studied during the post-monsoon season. Four different sites were studied for each lake. 12 replica of water samples were collected from each site of the lakes and environmental variables of water i.e. pH, temperature, dissolved oxygen, total alkalinity, conductivity, total hardness, nitrate, inorganic phosphorus, total solid matter and free CO2 were analyzed. Macrophyte floras were collected during field sampling with the help of a 1m×1m light wooden quadrat and herbaria were prepared following the standard technique. Altogether 10 quadrats (five paired quadrats) were plotted in each site of the study area. Data obtained from water analysis and macrophytes were analyzed by SPSS statistics 20 and CANACO version 4.5. Higher values of nitrate and inorganic phosphorus were found in Beeshazar Lake and Tamor Lake, i.e. 4.41 ±0.52 mg dm–3 and 2.93 ±0.29 mg dm–3, respectively. In most of the lakes, macrophyte species, mostly Eichhornia crassipes was found to be dominant in terms of the importance value index (IVI), whereas in Tamor Lake, Spirodela polyrhiza was dominant. All the studied lakes were in the hypereutrophic category on the basis of nitrate and phosphorus concentration. Runoff of polluted water with agricultural fertilizers, pesticides and untreated industrial discharge as well as domestic wastes from the Khageri canal and excessive growth of invasive macrophytes are major threats to the studied lakes. The luxuriant growth of invasive macrophytes like Eichhornia crassipes also revealed the productive nature of the lakes and they can be taken as ecological indicators of organic pollution.