The waterfowl populations that visit segments of the Rapti and Narayani Rivers in Chitwan National Park, Nepal were systematically counted from 2010 to 2019 to calculate yearly indices and population trends. Eighteen species of waterfowl were identified, out of which eight were regular visitors. Ruddy Shelduck (Tadorna ferruginea) was 80% of the total waterfowl population. The Rapti and Narayani Rivers provided winter habitat for 15.5% of the Ruddy Shelduck in the South Asian Flyway. Along with Ruddy Shelduck, these rivers individually and regularly supported more than 1% of the population threshold of Goosander (Mergus merganser) in the South Asian Flyway, designating the rivers in Ramsar Criteria 6 in the RAMSAR convention (Wetlands International 2017). Out of eight regular species, six species had an increasing population trend. The long-term trend of Ruddy Shelduck showed a strong increase in the annual rate of population change by + 10.14%. A strong increase was also shown by Bar-Headed Goose (Anser indicus; + 18.96%), Gadwall (Anas strepera; + 12.06%), Mallard (A. platyrhynchos; + 12.44%), and Common Teal (A. crecca; + 12%). Goosander (+ 4.94%) showed a moderate increase, while Lesser Whistling Duck (Dendrocygna javanica; - 12.85%), and Northern Pintail (A. acuta; - 10.80%) showed steep declines in their long-term trends. This work can provide a baseline for management and conservation of the waterfowl of Chitwan National Park, as there is no continuous data available there.