An acoustic navigation system includes a vessel and an interrogation unit towed behind the vessel below the surface of the water, a tail acoustic transponder trailing behind the interrogation unit, and a pair of surface acoustic transponders towed behind the vessel on the surface of the body of water. The interrogation unit generates an acoustic interrogation signal and receives responses from each of the tail acoustic transponder and the surface acoustic transponders from which it triangulates its position. The surface acoustic transponders may further include GPS receivers for receiving positioning information from GPS satellites. Additional acoustic transponders on instruments located on the floor of the body of water respond to the interrogation signal to allow triangulation of the location of the instruments.