The existence of a humic substance in water causes the growth of microorganisms and reduces the quality of water; therefore, the removal of these materials is crucial. Here, the ZnO nanoparticles doped using transition metals, copper (Cu) and manganese (Mn), were used as an effective catalyst for photocatalytic removal of humic substances in an aqueous environment under ultraviolet, visible light, and light-emitting diode irradiations. Also, we study the effect of the sonocatalytic method. A solvothermal procedure is used for doping, and the Cu- and Mn-doped ZnO nanocatalyst were characterized by means of FTIR, XRD, AFM, SEM, and EDAX analyses. We investigate the effect of operational variables, including doping ratio, initial pH, catalyst dose, initial HS content, and illuminance on the removal efficiency of the processes. The findings of the analyses used for the characterization of the nanoparticles illustrate the appropriate synthesis of the Cu- and Mn-doped ZnO nanocatalysts. We observe the highest removal efficiency rate under acidic conditions and the process efficiency decreased with increasing solution pH, when we tested it in the range of 3–7. Photocatalytic decomposition of HS increases with a rise in catalyst dose, but an increase in initial HS content results in decreasing the removal efficiency. We observe the highest photocatalytic degradation of humic acid while using the visible light, and the highest removal efficiency is obtained using Cu.ZnO. The Cu.ZnO also shows better performance under ultraviolet irradiation compared to other agents.