In topsoils, the activity concentrations of natural radionuclides (hereafter NRs) increase due to the addition of NRs from fertilizers, irrigation water, and air dust pollution. On the other hand, various physical-chemical and environmental processes such as radioactive decay, volatilization, leaching, erosion, and plant uptake were responsible for the decrease of the activity concentrations of NRs in the topsoils. In this study, behaviours of 40K, 210Pb, 226Ra, 238U, and 232Th in topsoils were modelled by the CEMC soil model and the HYDRUS-1D model. An exponential equation was proposed for estimating the accumulation rates of these radionuclides in the topsoils. Long-term accumulation of radionuclides was assessed for water spinach (Ipomoea Aquatica Forssk.) soil (hereafter VES) and rice (Oryza sativa L.) soil (hereafter RIS). We found that the current agricultural practices caused the increase of 40K activity concentration in the water spinach soil, and 40K, 210Pb, 226Ra, and 232Th activity concentrations in the rice soil. The accumulation rates of radionuclides were in the order 238U < 232Th < 226Ra < 210Pb < 40K. 25 years of cultivation with water spinach can increase/decrease + (165 ± 6) Bq of 40K, – (8.2 ± 0.7) Bq of 210Pb, – (4.3 ± 0.2) Bq of 226Ra, – (7 0.3 ± 0.3) Bq of 238U, and – (1.8 ± 0.1) Bq of 232Th in 1 kg soil. For rice cultivation, these values are + (1004 ± 39), + (3.3 ± 0.2), + (3.0 ± 0.2), – (5.1 ± 0.3), (2.2 ± 0.1) Bq kg−1 for 40K, 210Pb, 226Ra, 238U, and 232Th, respectively.