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Interactions among ions, molecules, and confining solid surfaces are universally challenging and intriguing topics. Lacking a molecular-level understanding of such interactions in complex organic solvents perpetuates the intractable challenge of simultaneously achieving high permeance and selectivity in selectively permeable barriers. Two-dimensional covalent organic frameworks (COFs) have demonstrated ultrahigh permeance, high selectivity, and stability in organic solvents. Using reactive force field molecular dynamics modeling and direct experimental comparisons of an imine-linked carboxylated COF (C-COF), we demonstrate that unprecedented organic solvent nanofiltration separation performance can be accomplished by the well-aligned, highly crystalline pores. Furthermore, we show that the effective, as opposed to designed, pore size and solvated solute radii can change dramatically with the solvent environment, providing insights into complex molecular interactions and enabling future application-specific material design and synthesis.