Coal-fired power plants (CFPPs) are the dominant source of electricity in South Africa due to natural abundance of coal in the country. However, emission of SO2, Pb, and Hg has raised serious environmental and public health concerns. Hence, to reduce emissions and utilize coal efficiently, estimating emission trend, understanding the forms of elemental occurrence in coals, and affinities to minerals, organic matter, and pyrite, are essential. Therefore, this paper aimed to assess the forms of elemental occurrence of sulfur, and Pb and Hg affinities to ash and sulfur, in the coals via statistical correlation and their isotopic compositions. This study also estimated SO2, Pb, and Hg emissions from 1971 to 2018 from the CFPPs on levels of activity and emission factors. Based on the results, South Africa coals mostly comprise equivalent fractions of organic and pyritic sulfur. The Pb were correlated with ash (R2 = 0.393), which is an indication of the presence of bound clay mineral. However, the highest Pb208/Pb206 and the lowest Pb208/Pb206 in South Africa coals which contain high inertinite (organic matter) and low sulfur, reveal organically associated Pb. Similarly, clay minerals associated Hg appeared based on its relationship with ash (R2 = 0.450), and the remaining could be an organic matter related. As an organic matter associated element least cleanability and readily oxidizing nature, burning South Africa coals containing a substantial quantity of organic sulfur and organically bound Pb and Hg without washing will obviously result to higher emissions. The estimated for SO2, Pb, and Hg emissions were 355.84 Gg, 168.91 tons, and 4.84 tons in 1971, and increased to 1468.13 Gg, 696.89 tons, and 19.95 tons in 2018, respectively. The values approximately increased by a factor of 4.