Nanofiltration membranes have limited ion-ion selectivity in water treatment applications, especially when separating ions with similar size and charge. To achieve greater size-based selectivity in nanofiltration, more control of pore structure is required during membrane fabrication. We demonstrate how to tailor membrane pore size and thickness using polyelectrolyte layer-by-layer assembly by alternately applying two strong polyelectrolytes, PDADMAC and PSS, to a polysulfone substrate while systematically controlling the polyelectrolyte and salt concentrations in the deposition solution. Results suggest that increasing polyelectrolyte concentration or salt concentration in the deposition solution increases polyelectrolyte multilayer thickness, but the effects on pore size may be categorized into two distinct regimes. In the first growth regime, increasing polyelectrolyte concentration in the deposition solution led to larger polymer deposition rates and smaller pore sizes. In the second growth regime, increasing polyelectrolyte concentration produced larger pore sizes. We attribute the second regime to less adsorbed polyelectrolyte on the membrane and/or less coiled polymer chains as a result of changing polyelectrolyte-salt interactions. Overall, results show that pore size modification is achievable using layer-by-layer assembly by tuning polyelectrolyte-salt interactions and can be used to study and improve size-based selectivity in membrane separation processes.