Carbon nanotube (CNT)-based filters have the potential to revolutionize water treatment because of their high capacity and fast kinetics in sorption of organic, inorganic, and biological pollutants. To date, CNT filters either rely on CNTs dispersed in liquids, which are difficult to recover and cause safety concerns, or on CNT buckypaper, which offers high efficiency, but suffers from an intrinsic trade-off between filter permeability and capacity. Here, a new approach is presented that bypasses this trade-off and achieves buckypaper-like efficiency combined with filter-column-like permeability and capacity. For this, CNTs are first assembled into porous microspheres and then are packed into microfluidic column filters. These microcolumns exhibit large flow-through filtration efficiencies, while maintaining membrane permeabilities an order of magnitude larger then CNT buckypaper and specific permeabilities double that of activated carbon for similar flowrates (232 000 L m-2 h-1 bar-1 , 1.23 × 10-12 m2 ). Moreover, in a test to remove sodium dodecyl sulfate (SDS) from water, these microstructured CNT columns outperform activated carbon columns. This improved filtration efficiency and permeability is an important step toward a broader implementation of CNT-based filtration devices.