Are global navigation satellite signals like GPS, Glonas, Navic, or Galelio received under water ? Can Radio frequency signals penetrate underwater ? Up to what depths ? If not then what sensor systems are used for navigation?
Under water you use inertial sensors, pressure sensors, ultrasonic modem, acoustic doppler velocimetry, ultrasonic sensors for obstacle detection and so on. For navigation the kalman-filter is very useful. Electromagnetic waves will not have a long range under water even at low frequency and big antennas. GPS can be used if you are over water to get the initial position and heading, but after diving you use the sensors mentioned above.
If it is a system that will operate in shallow water, we can include cameras in addition to the sensors mentioned by Marc Schmieger . Light and turbidity are a big problem for cameras. However, the solution is easier when looking at the problem in terms of SLAM with cameras and sensors mentioned.