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The South China Sea (SCS) is divided into two parts namely northern SCS (nSCS) and southern SCS (sSCS). The sSCS is a semi-closed system that receives rapid large water flushing from the Western Pacific Ocean and the Java Sea during the northeast and southwest monsoon events. Major natural radionuclides in sSCS are expected to come from river water and terrestrial sediment discharge i.e., Mekong River, Chao Phraya River, Pahang River and Rajang River which contain high lithogenic and biogenic materials. A box model was developed to estimate the amount of 232Th discharge from rivers to the sSCS basin. The result shows that the total flux of 232Th entering into the sSCS was 140.3 × 103 Bq/km2/yr, with the highest contribution from the Pahang River followed by the Rajang River, Mekong River and Chao Phraya River. The activity concentrations of natural radionuclides presented herein should be considered useful in order to understand the geochemical behavior of natural radionuclides in marginal sea areas. The review shows that publications on natural radionuclides are still limited; therefore further research needs to be done.