In the present study, the adsorption of two types of hazardous atoms including arsenic and lead with TON zeolite and bilayer silica (2D-SiO2) have been investigated by employing Ab initio-based density functional theory (DFT) calculations. To reach a full structural optimization and the most stable configuration, four sites were considered for TON zeolite as well as five sites for 2D-SiO2, and adsorption energy along with equilibrium geometry was determined. The adsorption energies of arsenic atom on the surface of 2D-SiO2 absorbents and TON zeolite have obtained equal to and − 1.25 eV and − 2.76 eV, respectively, which both of them are chemisorption type. We also found that the adsorption of lead on the surface of 2D-SiO2 was physisorption type with the adsorption energy accounting for − 0.13 eV, while the adsorption energy between lead and TON was calculated equal to − 2.32 eV which was chemisorption type. Furthermore, our results demonstrate that the TON zeolite was more capable of adsorbing hazardous atoms compared with 2D-SiO2 due to having greater adsorption energy. The adsorption of arsenic on the 2D-SiO2 and TON adsorbents is also stronger than those of lead atom. Furthermore, we modeled and considered graphene, as a common adsorbent nanostructure, to compare and validate the accuracy of our simulations and obtained results. Finally, the electronic density of states (DOS) calculations and charge analysis were done by the use of Mulliken method, and the results confirmed those results that had already been obtained from adsorption energies.