This work addresses a key challenge of tailoring the ion selectivity of a thin-film composite nanofiltration membrane to a specific application, such as water softening, without altering the water permeability. We modified the active surface of a commercial NF270 membrane by molecular layer deposition (MLD) of ethylene glycol-Al (EG-alucone). With increasing deposition cycles, we found that the MLD precursors first infiltrated and deposited in the active layer of NF270, then inflated the active layer, and finally deposited on the surface as a distinct EG-alucone layer. The deposition process changed the morphology of the membrane active layer and decreased the overall density of its fixed negative charge by embedding the positively charged EG-alucone. Filtration experiments revealed that these modifications affected the ion separation properties of the membrane without significantly hindering the water permeability. Specifically, the permeation of Na+ increased relative to that of Mg2+, as indicated by the permselectivity of Na+ salts over Mg2+ salts. The changes in permselectivities with an increasing number of MLD cycles were rationalized using the dielectric, steric, and electrostatic ion exclusion mechanisms, which are related to the membrane material, pore size, and fixed charge, respectively. These relations open a path for the rational design of nanofiltration membranes with tailored selectivity by tuning the properties of the MLD layer. Filtration results of natural brackish groundwater using the MLD modified membranes agreed with the single salt experiments. As a result, water hardness was 26% lower for the permeate obtained using the MLD-modified membranes, which were found stable even during a 24 h filtration run. These results highlight the practical potential of this approach in enhancing water softening efficiency.