I think UD has experimented with using acoustic modems. Chien-Chung Shen in CIS is an expert in that area. You have to cope very very long propagation delays. Our group is interested in these problems.
Mode 1: AUV surfaces and raises an RF antenna above the surface. Mode 2: a relay sits at the surface, the AUV talks to it acoustically, and the UAV over RF. Mode 2 is the most common. Typical relays are a gateway buoy, or a waveglider.
There are some solutions with directive lasers. High communication bandwidth van be achieved, but the positionnement precision , and stability of the station keeping requirements are important.