Despite the name, this base is not located in the suburban town of Waterkloof, Pretoria, but lies to the south of Pretoria, 4.34 nmi (8.04 km) to the northeast of Centurion, Gauteng and 3.37 nmi (6.24 km) from AFB Swartkop, at an elevation of 1506 metres (4940 ft).

On 30 April 2013 a flight full of Indian citizens who had come to attend a wedding of the Gupta family landed at Waterkloof airbase.

This was in contravention of South African law since the airbase is classified as a National Key Point; in theory not available to be used for personal air travel by unaffiliated private individuals.

[3] In April 2023 the President of the United Arab Emirates, Sheikh Mohamed bin Zayed Al Nahyan, and his family landed at the base during their vacation to a South African game lodge in the Eastern Cape.

[4][5] In May 2023, a year after Russia's 2022 invasion of Ukraine, a US-sanctioned Russian transport plane landed at the airport carrying an unknown cargo.