In order to detect the toxicity of algicidal products and valuate the harm of microcystin in the water source to the human body, the luminescent bacteria was to determine the toxicity, USEPA recommended model provided a health risk assessment of source water. The results show that the strain Y1 inhibit the growth of microcystis aeruginosa effectively. The strain had a slight toxicity to the luminescent bacteria. When the concentration of chlorophyll a was 34.92 mg/m³, the increase of dosage could enhance the toxicity of algae. The toxicity of liquid algae added bacteria was significantly lower than that of the control group, when the concentration of chlorophyll a was greater than 46.56 mg/m³. The non carcinogenic risked index of MC-LR in the water source was 2.89~4.87, which was reduced to 1.3 after BAF treatment, even to 0.6 after adding strain Y1. It reached health risk assessment safety standards when the the value was less than 1. Through the prediction model, it was found that the organic matter in treated water had no mutagenicity, it indicated that waters with strain Y1 had not biotoxicity and mutagenicity.