Here's a video from one of our recent tests of our GTQ-Cormorant: a submarine and quadrotor hybrid.
We use an air pump/solenoid system to move air between the clear, water-tight pressure hull and an external air bladder for depth control (down to around 7' in this test). An APM 2.5 controls SAS and pump/solenoid switching. We use the barometer onboard the APM as a depth sensor.
More details and videos will be posted soon: http://www.uavrf.gatech.edu/