Freshwater ecosystems cover only 0.8% of the earth’s surface, but they are amongst the most diverse systems in the world. They are vital for the life and well-being of billions of people as they provide different direct and indirect services. Our present focus of the study, the Koshi River basin (KRB), one of the largest tributaries to the Ganga River, is home to about 40 million people who depend on it for the ecosystem services. This basin is especially important to the people of Nepal, whose livelihoods and economic growth it supports. However, freshwater ecosystems in the KRB are changing because of various natural disturbances and human interventions. Moreover, limited knowledge is available on the status of its freshwater ecosystems. The assessment of the status of freshwater is crucial for managing, conserving, and restoring any freshwater ecosystem. Therefore, this study carried out a rapid assessment of the Koshi basin of Nepal to produce knowledge on the status of the river ecosystems in the basin.