An axial flow pump is a kind of high-specific revolution vane pump that has the characteristics of large flow, low head, and high efficiency. Due to its unique properties, it is widely used in large water diversion projects, such as the South-to-North Water Diversion Project. However, during the operation of the pump, some fish enter the axial flow pump together with the water flow through the screen before the entrance of the pump station. Consequently, some fish are inevitably damaged or even die in the process of traversing through the pump. Meanwhile, the decay of dead fish directly affects the quality of water, hence, posing serious ecological pollution and destabilizing the ecological balance. Therefore, understanding the dynamics of axial flow pumps in relation to fish species in water bodies for biodiversity and ecosystem services remain vital for nature conservation. In this paper, the impact of damage of the model pump on fish is exhaustively investigated according to the theory of blade impact model, impact probability, impact mortality, and mortality distribution under different working conditions. Through the simulation of the flow state inside the impeller, the areas that are lower than the pressure threshold, higher than the shear strain rate threshold, and higher than the pressure gradient threshold in the impeller at different flow rates are analyzed. Based on the unsteady results, the volume fluctuation characteristics of the three damage mechanisms in the impeller are analyzed. Furthermore, Powell vortex acoustic equation is used to locate the high noise source region of the axial flow pump. After extensive comparison of the dipole sound source intensity, it is revealed that the dipole noise source in the impeller and guide vane is dominant. In conclusion, this study provides a holistic perspective for evaluating fish damage caused by the flow in the impeller of the axial flow pump. Furthermore, it will proffer significant references to the construction of ecological water conservancy projects.