This study collected 21 soil samples from 30 to 120 cm depth, from 9 solid gold mine waste dumps in the Witwatersrand basin, South Africa. The samples were analysed using ICP-OES method to determine the concentrations of heavy metals. Principal component analysis (PCA) was performed to track sources of heavy metals, migration passages, their distributions and spatial variations at the study sites. The results of this study showed that the soil screening values (mg/kg) ranged from 2.20–7,070.00 Pb, 0.20–11.00 As, 0.06–2,630.00 Hg, 1.00–69.00 U, 0.02 − 4.20 Cd, and exceeded the background concentrations of the continental crust. The study results further showed that the average concentrations (mg/kg) of Pb (432.08), U (13.75), Tl (4.41), Ag (1.07), Cd (0.34) were highest at Durban Deep. Arsenic (59.86) and Sn (2.03) were highest at Krugersdorp, Kagiso, New Canada, and Shaft 17. The average values of Hg (625.56 µg/kg) and Au (17.67 µg/kg) were highest at Mogale City, Fleurhof, Krugersdorp, Shaft 17, and Davidsonville. These values reflected moderate to extreme contamination, supported by geoaccumulation index (Igeo), pollution load index (PLI), and contamination factor (Cf i) values. According to PCA, F1 was responsible for heavy metal generations from the local gold processing and waste dumping facilities. The F1 loading for Cd and Pb was 0.845 and 0.835, respectively, whereas F1 and F2 contribution of the variable % were greater than 0.70 for Ag, As, Au, Cd, Pb, Sn, Tl, and U, suggesting that they were generated from the waste dumps, transported by rain water and subsequently deposited in downstream soil. The heavy metal concentrations were traced upstream at the dumps where the highest averages were recorded, whereas the lowest values were measured from downstream samples. Thus, the gold mine tailing dumps are considered the primary sources of the high measured values of the heavy metals in the study sites. The ecological risk values were ranked in the order of As > Cd > Hg > Pb and exceeded the permissible health risk value suggested by the South African and global standards. Excessive Hg concentration with 160 ≤ E r i < 320 was recorded at Krugersdorp, whilst Pb with 320 ≤ E r i was recorded at Durban Deep. Thus, the estimated high E r i values insinuate higher ecological risk of heavy metals that can accumulate in the human body through absorption, inhalation and ingestion of dust, or ingestion of food grown from the contaminated soil.