Abstract The ship’s water injection system exhibits significant vibration and noise issues, necessitating the prompt implementation of targeted control measures. In this study, the simulation technique of computational fluid dynamics (CFD) combined with the finite element method and automatic matching layer method was applied to emulate the flow field environment of the outlet pipeline of a side valve in a seawater cooling system. Pulsating pressure data on the pipeline and valve’s wall were extracted from the flow field calculation and utilized as dipole noise sources and structural vibration excitations, enabling the prediction and separation of flow noise and flow-induced vibration noise in the water injection system. Leveraging the data from the flow field simulation, an analysis was conducted on the radiated noise at the side valve’s outlet, comparing the impact of different underwater depths and outlet pipe diameters on the underwater flow noise. The findings suggest that measures such as increasing the side valve’s diameter and lowering the discharge port’s underwater position can effectively reduce system flow noise, offering valuable insights for the design of noise reduction in seawater cooling systems for silent surface ships and submarines.