The biggest river of the National Park the Babrungas has its source from the lake of Plateliai; its length is 47,3 km, 10 km of them run through the territory of the Park. Though, the Uošna river is considered to be the longest on the territory of the Park (13,3 km of 16,6 km lay across the Park). Besides the mentioned rivers there are 32 rivulets , 17 of them of it run only across the territory of the Park. The total length of these rivultes is 103,5 km, approximately 30 rivulets have their source in the Park. The largest part of the rivers and rivulets of the National park (51%) have been reclaimed and straightened.
There are quite a few springs in the territory of the Park, some of them even have sacral meaning. Springs of Plokščiai (3,2 ha) and Pilelis (2,4 ha) are natural monuments. Visitors can easily reach the springs of St. John and Pilelis.