There are several rivers and lakes in Thoubal. The most important rivers traversing through the district are Imphal and Thoubal. These two rivers serve as the lifeline to the many villages and towns of the district and also add to the natural beauty of the place.
Among the lakes, the most prominent ones are Ikop Lake, Lousi Lake, Pumlen Lake and the Waithou Lake. Ikop Lake is a popular tourist destination mainly because of the abundant nature around the lake. The cool breeze on the high altitude makes a visit worthwhile. Lousi Lake is spread over an 18 sq.km area and is popular among geologists. The lake boasts of a tender ecosystem. The water from the Lousi Lake is used for drinking by the locals.
The Pumlen Lake, also called the Pumlen Pat, is a freshwater lake in Thoubal. The main attraction here is the Phumdis or the floating decomposed plants.