There are a variety of ways to make a water tight vessel that can be opened once on the surface. Why not just make it so you can open it up.... then plug in the cable?
Depending on how deep you want to go some boxes off the shelf will go 20 or 30 feet down..... the only issue is penetrating wires into the box. but there is always a way that's much less headache than trying to load sketches via bluetooth.
check this guys site out. pretty good ideas and a forum all about ROVs with some decent info.
*edit - for example. Just found a depth sensor on their forum that the guys said he paid just a few dollars for and reads with an arduino. http://www.hoperf.com/upload/sensor/HSF1000-TQ.pdf
these are the ones i work on.... http://www.oceaneering.com/rovs/