This work reports a carbon nitride with pyridinic nitrogen-vacancy (N2CV-CN), which purifies organic contaminants via an in-situ photo-self Fenton-like reaction. Experiments and calculations demonstrated that the nitrogen-vacancy induces lone-paired (LP) and symmetry-unpaired electrons, promoting the formation of low-energy LP-π hybridized orbitals and helping to overcome the pairing energy required for oxygen to accept electrons. Furthermore, the nitrogen-vacancy accelerates film and intra-particle diffusion rates of organic contaminants on N2CV-CN, creating beneficial conditions for reactive oxide species to mineralize organic contaminants. Under sunlight and atmospheric oxygen, a photo-self Fenton-like reaction involving proton-coupled electron transfer occurred on the surface of N2CV-CN. Furthermore, by integrating photocatalysis with flocculation, about 99.1 % suspended substance, 45.5 % chemical oxygen demand, and 38.4 % biological oxygen demand were reduced from polluted river-water. Constructing N2CV-CN and understanding its crucial role offer theoretical and methodological insights into the in-situ purification of contaminated water bodies.