Photocatalytic processes driven by visible-light irradiation offer a sustainable means of micropollutants removal from aquatic environments without the addition of reagents. In this study, an enhanced production of photogenerated carriers under visible light has been achieved using acidified graphitic carbon nitride (ag-C3N4) modified with atomically-dispersed Cu (Cu/ag-C3N4), which serves as an efficient photocatalyst for treating mi/’cropollutants. The optimized Cu/ag-C3N4 system achieved greater than 90% micropollutants removal efficiency within 30 min. A combination of experimental testing and density functional theory analysis has confirmed the formation of an active and stable CuN3 configuration, generated by the incorporation of atomic Cu species at C vacancies that effectively modulates surface charge redistribution and enables charge separation. The photocatalytic degradation of micropollutants is promoted by photogenerated holes (h+) in tandem with reactive oxygen species (·OH, O2¯·, 1O2), where O2¯· and 1O2 species play dominant roles in the Cu/ag-C3N4 system. The application of ultra-performance liquid chromatography-tandem mass spectrometry analysis has been used to identify possible degradation pathways and establish a synergistic degradation mechanism. This work provides a comprehensive understanding of heteroatom doping that enhances photocatalytic activity, offering a new strategy in designing highly efficient photocatalysts for treating micropolluted water.