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Eichhornia crassipes and Monochoria vaginalis are waterweeds, and their uncontrolled proliferation in fresh and brackish water habitats is a serious ecological problem in many parts of the world. These weeds are quite common in the Vembanad Lake System (VLS), India's second-largest Ramsar wetland. During the non-monsoon season, the Thannermukkom saltwater barrage divides the VLS into two zones: saline water downstream and freshwater upstream. The field sampling of the current study was carried out in the upstream zone of the VLS during the Pre-Monsoon (March 2017). Fresh Eichhornia and Monochoria samples were collected, transported to the lab, and experiments were conducted under natural light conditions to determine how much extra water they transpire into the atmosphere. The results showed that the water loss in experimental tanks with Eichhornia (evapotranspiration) is roughly twice that in control tanks without them (only evaporation). Monochoria transpires fairly more water to the atmosphere than Eichhornia. These results reveal that the proliferation of waterweeds has a significant adverse effect in conserving water in all freshwater bodies infested with them. The current study also points out that the expansion of waterweeds has the potential to worsen drought conditions as they cause excess water loss into the atmosphere and a faster drying up of freshwater reservoirs. Two possible approaches for managing the waterweeds in the VLS include reducing nutrient loading upstream and more frequent opening of the Thannermukkom saltwater barrage to allow saltwater intrusion, which could inhibit the growing waterweeds., (© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)