Over the years, the Phiphidi sacred natural site has been protected by traditional methods or cultural codes. However, over the past three decades, anthropogenic pressures have affected the site. This study aimed to investigate the historical uses of the Phiphidi sacred natural site and contemporary anthropogenic threats to the area, and the implications on the sustainability of the area. The data supporting this study were collected between June 2018 and May 2021, during which (i) interviews, (ii) observations and (iii) documents were used as the main techniques of data collection. Non-probabilistic purposive (also known as judgemental) sampling was used to select respondents including the custodians of the Phiphidi sacred natural site, officials working at Phiphidi Waterfall, representatives of the Dzomo La Mupo committee and local communities. The data obtained from interviews were analysed using thematic content analysis. Field observations helped in validating the data that were collected through interviews. The study showed that although the sacred site was historically a ‘no go area’ and was used to connect with ancestors and perform rituals, contemporary anthropogenic threats affecting the Phiphidi sacred site include weak property right systems and tourism infrastructure development that has led to land-use conflicts that have been driven by vested interests. The contemporary practices not only undermine the Vhavenda culture but also have negative implications for the biodiversity of the area. In addition, the current practices undermine the founding principles of the 1996 Constitution of the Republic of South Africa; these embrace culture, religion and the country’s environmental laws. While passion to save the sacred sites by custodians and local communities is still alive, government support is weak and, as a result, there are fears that other sacred sites in the region may also be targeted for tourism purposes. Several suggestions are made that, if implemented, could help to protect the remaining sacred natural sites.