Current methods for electrocatalytic destruction of nitrate in drinking water require metal catalysts to achieve sufficient nitrate removal. However, metal-based catalysts involve complicated synthesis, increase treatment costs, and can lead to leaching of metals into treated water. In this study, we achieved nitrate reduction performance comparable to that of metal-based catalysts via electrofiltration through a metal-free nanoporous electrified membrane (EM) containing unmodified pristine carbon nanotubes (CNTs). Experimental results coupled with computational fluid dynamics simulations elucidated how the decreased diffusion boundary layer in the flow-through CNT-EM mitigates diffusion limitations to enhance overall reaction activity. A maximum single-pass removal efficiency of 86.9% was reached for an initial nitrate concentration of 10 mM when the mass transport rate matched the reaction rate. Through density functional theory and molecular dynamics calculations, we demonstrated enhanced *NO2 and *NO adsorption energies at intrinsic defect sites, which are present in most commercial CNTs and become more accessible to nitrate ions under flow-through operation. Finally, the long-term stability, tolerance of environmental interferences, and sufficient nitrate removal and N2 selectivity to meet drinking water standards were demonstrated in synthetic surface water. By elucidating how nanoporous electrofiltration enables dynamic matching of reaction and transport rates, this study demonstrates a new strategy to drastically improve electrocatalytic reaction performance without complex catalyst materials innovation, bridging existing gaps for nitrate removal in drinking water treatment related to the use of metal-based catalysts.