Two-dimensional (2D) covalent organic frameworks (COFs) are composed of structurally precise, permanently porous, layered macromolecular sheets, which are traditionally synthesized as polycrystalline solids with crystalline domain lengths smaller than 100 nm. Here, we polymerize imine-linked 2D COFs as suspensions of faceted single crystals in as little as 5 min at moderate temperature and ambient pressure. Single crystals of two imine-linked 2D COFs were prepared, consisting of a rhombic 2D COF (TAPPy-PDA) and a hexagonal 2D COF (TAPB-DMPDA). The sizes of TAPPy-PDA and TAPB-DMPDA crystals were tuned from 720 nm to 4 μm and 450 nm to 20 μm in width, respectively. High-resolution transmission electron microscopy revealed that the COF crystals consist of layered, 2D polymers comprising single-crystalline domains. Continuous rotation electron diffraction resolved the unit cell and crystal structure of both COFs, which are single-crystalline in the a-b plane but disordered in the stacking c dimension. Single crystals of both COFs were incorporated into gas chromatography separation columns and exhibited unusual selective retention of cyclohexane over benzene, with single-crystalline TAPPy-PDA significantly outperforming single-crystalline TAPB-DMPDA. Polycrystalline TAPPy-PDA exhibited no separation, while polycrystalline TAPB-DMPDA exhibited poor separation and the opposite order of elution, retaining benzene more than cyclohexane, indicating the importance of improved material quality for COFs to exhibit properties that derive from their precise, crystalline structures. This work represents the first example of synthesizing imine-linked 2D COF single crystals at ambient pressure and short reaction times and demonstrates the promise of high-quality COFs for molecular separations.