Bulk chemical oxygen demand (COD) remains the main basis for managing organic carbon in wastewater treatment, yet it does not distinguish readily biodegradable carbon from dissolved organic carbon (DOC) that persists over treatment timescales. This can lead to unnecessary treatment intensity and associated greenhouse gas (GHG) emissions. Here we characterized size-dependent DOC persistence in a full-scale anaerobic–anoxic–oxic wastewater treatment plant by combining size-fractionated bioreactivity measurements with optical spectroscopy, FT-ICR MS, metabolomics and microbiome analyses. Two operational thresholds were identified: ~0.7 μm, separating most labile particulate and colloidal carbon from a more persistent dissolved pool, and 30 kDa, isolating the least biodegradable low-molecular-weight fraction. Although total organic carbon removal exceeded 90%, residual effluent organic matter was concentrated mainly in the <30 kDa pool and showed limited short-term biodegradability. Molecular data indicate that this persistence was associated with selective retention of carboxyl-rich alicyclic molecules and depletion of nitrogen-rich saturated compounds, rather than increasing aromaticity. Across the treatment train, removal of 39.2 mg L⁻¹ operationally persistent carbon accounted for 49.7% of total carbon removal. Scaling with data from 63 municipal plants in 12 countries suggests that preserving this persistent fraction could reduce GHG emissions by 20.2–60.6 Mt CO₂-eq yr⁻¹ under an operational methane baseline, and by 84.2–253 Mt CO₂-eq yr⁻¹ under an IPCC-style upper-bound framework. These results suggest that wastewater treatment can move beyond bulk carbon removal toward size-resolved management based on carbon reactivity and environmental fate.