An array of ion separation cells is presented in this work, to propose a novel desalination device. Molecular Dynamics simulations have been incorporated to establish the theoretical background and calculate all parameters that could lead the manufacturing step. The main system component is an ion separation cell, in which water/NaCl solution flows due to an external pressure difference and ions are directed towards the non-permeable walls under the effect of an electric field, with direction perpendicular to the flow. Clean water is gathered from the output, while the remaining, high-concentration water/ion solution is re-cycled in the cells. The strength of the electric field, cell dimensions, and wall/fluid interactions are investigated over a wide range, and shear viscosity and the volumetric flow rate are calculated for each case.