The quantile regression method has been applied to examine the relationship between different concentrations of Fe²⁺ and S^2- with velocity and Dissolved Oxygen (DO) in the black bloom region on the Nanfei River estuary of Chaohu Lake. Unlike linear regression, quantile regression can quantitatively analyze the effect of flow velocity and DO on different concentrations of Fe²⁺ and S^2-. Analysis showed that the flow of water reduces the concentration of Fe²⁺ and S^2- by dispersion. The effect of increasing velocity significantly reduced the concentration of Fe²⁺ and S^2- in the Nanfei River estuary and the edge of the black bloom where the concentration gradient was high. However, there was hardly any effect on the reduction of Fe²⁺ and S^2- pollution in the middle of the black bloom region where the concentration gradient was low. Increasing the DO concentration reduced the S^2- pollution if the concentration was above 0.043mg/L. It also decreased the Fe²⁺concentration when it was above 0.80mg/L. Conversely, the treatment of low concentrations of Fe²⁺ and S^2- were little. These results provide a theoretical basis for the management of black blooms in shallow lakes.