This dataset contains gridded total water storage changes (TWSC) over South Africa, derived from daily Global Positioning System (GPS) uplift data. The TWSC are available monthly, with a grid resolution of 2°x2°, for the period from September 2000 to April 2021 and contain only long-term variations as well as annual and semi-annual oscillations. The post-processing of the GPS data included the removal of offsets, data gaps, and outliers, as well as the reduction of short-term variations and noise by employing singular spectral analysis (SSA). Utilizing Green's functions with load Love numbers for the Preliminary Reference Earth Model (PREM), the monthly averaged GPS uplifts were inverted to derive the water mass load with respect to January 2017. In addition, the refined GPS uplift observations in South Africa are also provided.