This dataset contains vegetation and soil data collected from wetlands in the upper catchment of the Mokolo River in the Waterberg region, Limpopo Province, South Africa. The study aimed to characterise wetland vegetation types and examine relationships between vegetation composition and soil physicochemical properties within a Strategic Water Source Area. Vegetation data were collected following the National Wetland Classification System, with plant species composition and abundance recorded across multiple wetland sites. A total of 71 plant species from 28 families were identified and classified into seven distinct wetland vegetation types. Soil samples were collected at corresponding sampling points and analysed for physicochemical properties, including pH and concentrations of major cations and metals (e.g. Ca, Mg, Fe, Al, Cu), as well as organic carbon. Data are provided as comma-separated value (CSV) files, including vegetation species data and soil variables.