A noise cancellation system and method for use with a seeker head of a marine vessel are provided according to the invention. The seeker head employs one or more hydrophones that generate one or more output signals. The noise cancellation system includes a plurality of motion sensors. The plurality of motion sensors generate a plurality of noise signals based on a hydrodynamic flow noise caused by the marine vessel and acting on the marine vessel. The noise cancellation system further includes a processor receiving the plurality of noise signals and the one or more output signals and applying an active noise cancellation to the one or more output signals to substantially cancel out the flow noise. The active noise cancellation is based on the noise signal.