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A pilot-scale drinking water treatment process for Songhua River, including conventional treatment (coagulation-settlement and rapid sand filtration), ozonation, biological enhanced activated carbon (BEAC) filtration, and chlorination disinfection, was carried out in this study. To investigate the impact of ozonation and BEAC filtration on removing the composition of micropollutants in drinking water, we detected the micropollutant composition from each stage of the treatment process by non-targeted analysis using a GC-MS technique and compared the results between effluents of single BEAC and O-BEAC processes. Aromatic compounds and esters could be abated efficiently during single BEAC filtration via biodegradation and adsorption; however, possible metabolic products (i.e., alkenes) were formed by biodegradation. Comparatively, O-BEAC process could reduce micropollutants much more significantly than single BEAC process especially for aromatic compounds including substituted benzenes and polycyclic aromatic hydrocarbons (PAHs) without the formation of metabolic products through the coupling effect of oxidation, biodegradation, and adsorption, suggesting that ozonation improved the removal potential of micropollutants in the BEAC process. In addition, conventional and novel chlorinated disinfection by-products were also measured during post-chlorination.