Discharge of wastewater containing nitrate (NO3−) disrupts aquatic ecosystems even at low concentrations. However, selective and rapid reduction of NO3− at low concentration to dinitrogen (N2) is technically challenging. Here, we present an electrified membrane (EM) loaded with Sn pair-atom catalysts for highly efficient NO3− reduction to N2 in a single-pass electrofiltration. The pair-atom design facilitates coupling of adsorbed N intermediates on adjacent Sn atoms to enhance N2 selectivity, which is challenging with conventional fully-isolated single-atom catalyst design. The EM ensures sufficient exposure of the catalysts and intensifies the catalyst interaction with NO3− through mass transfer enhancement to provide more N intermediates for N2 coupling. We further develop a reduced titanium dioxide EM as the anode to generate free chlorines for fully oxidizing the residual ammonia (<1 mg-N L−1) to N2. The sequential cathode-to-anode electrofiltration realizes near-complete removal of 10 mg-N L−1 NO3− and ~100% N2 selectivity with a water resident time on the order of seconds. Our findings advance the single-atom catalyst design for NO3− reduction and provide a practical solution for NO3− contamination at low concentrations. The selective and rapid reduction of nitrate at low concentration is technically challenging. Here, the authors report an electrified membrane loaded with Sn pair-atom catalysts that realizes near-complete removal of 10 mg-N/L nitrate and ~100% N2 selectivity during electro-filtration.