<p>Single-atom catalysts (SACs) demonstrate exceptional catalytic activity, yet their practical deployment in water treatment remains hindered by instability, scalability barriers and incompatibility with existing infrastructure. Here we present a hierarchical cross-scale assembly of manganese SACs confined within the nanopores of a ZrO₂ ceramic membrane (Mn-SA@CM), enabling scalable deployment for advanced water treatment. Validated in a pilot-scale device treating 1,200 litres of real hospital wastewater, Mn-SA@CM achieves an exceptionally high decontamination rate (9.8 × 10⁴ min⁻¹) and ultrahigh permeability (150 l m⁻² h⁻¹ bar⁻¹), overcoming the permeability–reactivity trade-off. This hierarchical design integrates metal–organic framework-derived micropores to stabilize atomic sites, membrane nanopores to drive advection-enhanced mass transfer and macroporous ceramic supports to ensure mechanical durability. Nanoconfinement inside the membrane pores concentrates reactants near catalytic sites, boosting degradation kinetics by 10⁵-fold compared with bulk systems. The membrane also exhibits self-cleaning functionality, sustaining &gt;97% removal of emerging contaminants over 168 h with negligible flux decline or metal leaching. By bridging atomic-scale catalysis with macroscale engineering via cross-scale assembly, this work establishes a viable, infrastructure-compatible platform for deploying SACs in real-world environmental remediation and beyond.</p>