Ba Be National Park is centred on Ba Be lake. The name Ba Be means "three lakes", although the lake is one continuous water body, 8 km long and up to 800 m wide. At an altitude of 178 m, Ba Be is the only significant natural mountain lake in Vietnam. It is up to 29 m deep, and contains numerous small limestone islets.
The site ranges in altitude from 150 to 1,098 m. The geology of the area is predominantly limestone, with numerous rugged peaks and deep, steep-sided river valleys. The limestone karst landscape contains many caves, the largest being the 300 metre-long Phuong cave, through which the Nang river passes.
Ba Be lake is fed by the Ta Han, Nam Cuong and Cho Leng rivers, which form the above-ground hydrological system in the southern part of the national park. The lake drains into the Nang river, which flows through the north of the park. The Nang river then flows southwards, eventually meeting the Lo river in southern Tuyen Quang province, before joining the Red River west of Hanoi.