• Simulated the effect of topology and pore size of zeolites on water purification. • Compared porous LTA, FAU, and MFI zeolites in purification of Cl - , Pb 2+ , and Co 2+ . • Tersoff and Lennard-Jones hybrid force fields, and TIP3P water models were used. • Applying PMF in MD simulation, the efficiency of zeolite membranes was conceptualized. • Applying a long time of 15 ns, heavy metal ions behaved differently in rejection. The efficiency of pollutant rejection (PR, %) and water purification of the zeolite membranes is highly dependent on their topology, i.e., porosity and chemical composition. Nevertheless, mechanisms controlling such a physicochemical phenomenon have been limitedly discussed. Herein, we provide insights into the physics and dynamics of water purification by zeolite nanosheets in terms of topological variables. The molecular dynamics (MD) simulation pictured the molecular-lever water purification having heavy metal ions (Co 2+ and Pb 2+ ) as typical water contaminants. Three siliceous zeolites having different topologies, i.e., LTA, FAU, and MFI zeolites, were positioned in the simulation space. MD simulation was served under pressure and temperature of 24 MPa and 300 K, respectively, applying the Canonical ensemble (NVT) condition. The intermolecular interactions between contaminant ions, zeolite, and graphene were tracked by hybridizing Tersoff and Lenard-Jones potentials, while the TIP3P model of the CHARMM force field was used to simulate water dynamics. The LAMMPS software and Visual Molecular Dynamics (VMD) were used to collect data and graphics over 15 ns, with early 5 ns devoted to reaching equilibrium. Interestingly, we demonstrated by the aid of potential of the mean force (PMF) pollutant ions which encounter the zeolite pores smaller than their kinetic diameter consume more energy for permeation across the membrane, -reason why LTA appeared selective against Pb 2+ , Co 2+ , and Cl - ions, with PR of 40, 60, and 100%, respectively. The absolute water flux values were monitored, and LTA and FAU fluxes were ∼ 50% higher than MFI zeolite, but 5 ns after equilibrium, LTA flux was overtaken sharply by the simulation because of the larger pore size. Overall, the electrostatic forces showed absolute control over the purification but were governed by the zeolite topology.