Lapalala is bisected by the perennial Palala river that drains the area from south to north. The most important tributary to the Palala River is the perennial Bloklands Spruit. A network of smaller streams drains the area along a conspicuous block-like fracture pattern into the Palala and Bloklands. These lines represent intrusive dykes that have weathered faster than the surrounding sandstone.

A number of dams have been built on the Bloklands and on minor streams. Although access to the rivers is sometimes difficult as a result of the steep topography, Lapalala can be considered as being well-watered. A full 72.8% of the property is within 4 km of the two main rivers, with 23.1% between 4 and 8 km and only 4.0% further than 8 km from water.

Seeps and wetlands occur extensively. The porous, sedimentary sandstone bands form good aquifers that hold water like giant sponges, slowly releasing it. Water levels fluctuate dramatically, depending on the current season's as well as previous season’s rainfall.