Linux-Based Autonomous Sub Leads Malaysia Airlines Flight Search
It would appear that the Bluefin-21 now searching the Indian Ocean offers a similar, but perhaps more powerful computing system. Bluefin lists a 4GB flash drive, plus additional payload storage. The craft also incorporates GPS, RF, Iridium, and strobe communications, and can connect via Ethernet at short range for downloading data at shipside. Other features include a dead-reckoning drift that is typically less than 0.1 percent of distance traveled.
Linux has figured in a variety of autonomous aquatic craft, including the Liquid Robotics' solar-powered Wave Glider SV3, designed in part by Java creator James Gosling. On the low-end, you can go underwater (with a tether) with the BeagleBone Black based OpenROV UUV.