Parthenium hysterophorus weed is an invasive noxious weed with a high growth rate and spread which can be attributed to its adaptability to a variety of soil types and climatic conditions. Its hazardous impacts on human health, livestock and agricultural crops have been documented, and so have the mechanical, cultural, chemical and biological techniques of its control. However, few studies have investigated possible impacts of Parthenium on the hydrology of a river basin, either qualitatively or quantitatively. This study aimed to quantify the effect of a Parthenium invasion on water balance components at a river basin scale. Penman-Monteith Evapotranspiration modeling indicated that Parthenium has lower evapotranspiration losses as compared to ASCE reference grasses and indigenous agricultural crops. Modeling the invasion of the Punpun river basin by Parthenium using the SWAT model re-established the tendency of Parthenium to transpire less, except during soil stressed conditions where Parthenium infested soil had a reduced moisture loss, which led to a short period of higher evapotranspiration losses compared to agricultural land cover just before the onset of monsoons. Further, the modeling results suggested that Parthenium invasion does not have a significant effect on surface discharge and groundwater recharge at a basin scale. The study recognized that precisely measured plant physiology parameters of Parthenium would be needed to understand its impact on the hydrology of a basin with lesser uncertainty. Lysimeter experiments under a controlled environment are recommended to overcome some of the existing gaps in our present understanding of Parthenium.