I've been fairly rough with my Kinects in experiments and teardowns but I never thought of drowning them!
If you take a look at the IR video from the v1/v2 you may see the problem when scanning water with near infra red light. The wavelength of IR used by the Kinect would get absorbed by the water more than visible light, and the surface of the water would reflect
a lot of the signal back anyway.
Do you see anything in the depth data from submerged objects at any distance?
I'm not sure the best way to get small object underwater scanning would be a Kinect. I would suggest a camera that uses stereo optical cameras like the ZED cam https://www.stereolabs.com/ or perhaps the intel r200 http://click.intel.com/intel-realsense-developer-kit-r200.html (I
think this has a passive (non IR) stereo mode for depth in addition to its active IR based structured light mode, but dont quote me on that)