<p>The development of nanofiltration (NF) membranes combining high water permeability with precise ion selectivity remains limited by the permeability–selectivity trade-off of conventional polyamide (PA) thin-film composite membranes. Herein, a nitrogen-rich imine-linked covalent organic framework (COF) was incorporated into the PA selective layer via interfacial polymerization to regulate membrane structure and ion transport. Structural characterization confirmed COF formation and its integration into the PA layer. COF incorporation enhanced membrane hydrophilicity, decreasing the water contact angle from ~ 62° to ~ 30°, which is attributed to COF-derived polar nitrogen-containing groups and AFM-confirmed surface roughening. Pure water flux also increased from ~ 43 to 50 L m⁻²&#xa0;h⁻¹. The COF-modified membranes exhibited improved desalination performance with a rejection order of MgSO₄ &gt; Na₂SO₄ &gt; MgCl₂ &gt; NaCl. At the highest COF loading, MgSO₄ and Na₂SO₄ rejection reached ~ 99% and ~ 98%, respectively, while MgCl₂ and NaCl rejection increased to ~ 50% and ~ 43%. Although zeta potential became less negative after COF incorporation, rejection improved, indicating combined contributions from hydrated ion size exclusion, PA-layer modification, enhanced wettability, and ion–framework interactions. Density functional theory calculations revealed stronger electronic perturbation and preferential interaction for sulfate-containing systems than chloride-containing systems, consistent with the experimental ion-selectivity trend.</p>