Radiochemical separation techniques were applied to measure 210Pb radioactivity in the samples to determine spatial distribution of total 210Pb radionuclide in surface sediments and water column for the main waters on the Sunda Shelf. The average 210Pb radioactivity level recorded from the Malacca Strait (MS) is significantly higher than the southern South China Sea (sSCS); this is attributed to the supply of input from the Andaman Sea in its northern areas, and massive terrestrial processes from bordering land masses. The results reveal that the decreasing trend of total 210Pb in Peninsular Malaysia’s marine sediment starts with the north maritime zone of Malacca Strait (64.28 ± 5.97 Bq/kg) > south maritime zone of Malacca Strait (50.88 ± 6.15 Bq/kg) > east maritime zone of sSCS (41.01 ± 3.07 Bq/kg) > south maritime zone of sSCS (40.78 ± 3.16 Bq/kg). The Kelantan and Pahang Deltas have been identified as two of the main anthropogenic sources of input for total 210Pb in the sSCS while atmospheric transboundary mobilization affecting total 210Pb in water column. In the Malacca Strait, however, the distribution of total 210Pb might be influenced mainly by in situ processes of the strait’s seafloor and sources origin of sediment.