Cuc Phuong National Park lies at the south-eastern extent of a limestone range that runs north-west to Son La province. This limestone range predominantly comprises karst, marine in origin and perhaps 200 million years old. The section of the limestone range encompassed by the national park rises sharply out of the surrounding plain, to elevations of up to 636 m. This section is around 10 km wide and 25 km long, and has a central valley running along almost the entire length.
The karst topography exerts a dominant influence on drainage patterns in Cuc Phuong. Most of the water that the national park receives is quickly absorbed by a complex underground drainage system common to mature karst landscapes, often emerging from springs on the lower slopes flanking the national park. For this reason, there are no natural ponds or other standing bodies of water within the national park, and there is only one permanent watercourse, the Buoi river. This river bisects the western end of the national park from north to south, and feeds the Ma river, the major river in Thanh Hoa province.