Soil contamination by many kinds of anthropogenic operations, such as industrial and mining activities, results in the accumulation of various heavy metal contaminants in the environment. Cadmium (Cd) and lead (Pb) are commonly found heavy metals in the Mahad Adahab mining area in Saudi Arabia. In this study, natural and modified zeolite sediments were fractioned by size to nano- and macrosizes and were applied to stabilize Cd and Pb from contaminated mining soil. Among the tested adsorbents, zeolite sediment in the nanosize that was modified by layered double hydroxides (LDH-N) showed the highest sorption and removal efficiency (>98%) for Cd and Pb, followed by nanosized natural zeolite (NZ-N) and HCl-modified nanosized natural zeolite sediment (HCl-N), which removed >90% Cd and Pb from contaminated soil. A pH of 7 was found to be optimal for Cd and Pb sorption, and the kinetics study revealed that first-order and pseudo-second-order kinetic models best fitted the experimental data (R2 = 0.94–0.98) for Cd and Pb sorption by the tested sediments. An incubation period of 16 weeks revealed that LDH-N, HCl-N, and NZ-N reduced the ammonium acetate extractable fraction of Cd by 89.26, 83.70, and 80.54% and Pb by 86.19, 81.42, and 77.98%, respectively. Electrostatic interaction and ion exchange were found to be the principal mechanisms for Cd and Pb sorption. The findings of this study indicate that the utilization of modified zeolite sediment in the nanosize fraction (LDH-N, HCl-N, and NZ-N) could be an effective and feasible strategy in stabilizing heavy metals and mitigating their toxicity in contaminated mining soil.