One of the most challenging thing about submarine communications is that EM waves don't propagate through water. To communicate from the surface to a submarine, we use radio waves on the order of 100Hz, with incredibly large antennas running at very high power. Submarines cannot communicate back without sending a more conventional antenna up to the surface.

Acoustics is the entire game under water. You can only detect nearby objects with visible light or sound. A great deal of submarine design goes into minimizing the amount of sound emitted into the environment because water is astonishingly good at transmitting sound waves very long distances with little loss.