Practical applications of heterogeneous advanced oxidation processes for organic pollutant destruction remain elusive due to poor yield of reactive oxygen species (ROS) as well as their ultrashort lifetimes and mass transfer limitations. To address these issues, nanoconfined catalysis, whereby improved reaction efficiency is attained due to rapid mass transfer, has recently gained traction in environmental remediation. Here, we introduce a simple concept of functionalizing the boron nitride nanosheet (BNNS) membrane, involving nucleation of cobalt nanocatalysts within the membrane intralayer network of water transport nanochannels. Membrane-confined crystalline reactive species with multiple exposed active sites spontaneously activate peroxymonosulfate, producing ROS for ultrafast (∼80 ms) destruction of organic pollutants at a fast flow rate of 548 L m−2 h−1. Co-BNNS membrane showed good stability and outperformed previously developed membrane-confined catalysis systems (up to 26-fold higher permeance). Co-BNNS membrane enabled ultrafast destruction of several organic pollutants, offering an attractive alternative for membrane-based catalysis applications.