Cladocera zooplankton as carriers of bacteria result in biological risk due to their occurrence in drinking water treatment systems. In this paper, bench-scale experiments were performed to investigate the inhibition effect on Daphnia magna (D. magna) by controlling its phototactic behavior. The results showed that UVA had a negative effect on the phototaxis of D. magna, indicating an active movement away from light source, while blue light was positive in inducing phototactic behavior. The water quality could influence the phototactic behavior of D. magna. When the turbidity value was higher than 10 NTU or total organic carbon (TOC) concentration was beyond 4 mg/L, the phototaxis of D. magna to UVA (25 μw/cm2 intensity) or blue light (1,000 Lux intensity) was significantly weakened. It was difficult for D. magna to offset the effect of water flow by its phototactic movement when the flow rate was higher than 10 mm/s. According to the above results, with suitable process parameters in full-scale experiments, the occurrence of D. magna in the effluent of sedimentation tank and activated carbon filter was obviously inhibited by the UVA irradiation and blue light induction, respectively.