There is growing interest in designing nanofiltration (NF) membranes for selective separations. However, controlling the formation process of polyamide (PA) membranes to achieve simultaneous improvements in permeance and selectivity remains challenging. The use of an interlayer has recently emerged as a promising strategy to tackle this tradeoff. Herein, nanoporous covalent organic framework (COF) interlayers were employed to facilitate the formation of a thin PA selective membrane layer. The COF interlayers were synthesized through a counter-diffusion IP method, during which the solvent and catalyst were tailored to achieve different extents of COF crystallinity. PA membranes made by conventional IP on these COF interlayers were found to show better performance than that made on a pristine polymer support. In addition, crystalline COFs resulted in a PA layer featuring a narrow pore size distribution and a high negative surface charge. The resulting dual-layer membrane exhibited enhanced NF performance, with superior rejection for divalent salts (Na 2 SO 4 , 99.6%; MgSO 4 , 97.4%), enhanced selectivity for mono/divalent salts (NaCl/Na 2 SO 4 , 137), and high water permeance. The combined permeance and selectivity exceed those of most reported NF membranes, making the PA/crystalline COF dual-layer membrane promising for NF-based selective separation.