The Underwater Jet is one of the most difficult vehicles to handle. Luckily it is voluntarily. You can also reach everything swimming and diving, although the Underwater Jet will make the journey much shorter and you can use it's handy weaponry (it uses Harpoon Gun ammo).
A similar vehicle, the underwater sled, is also present in the Cradle of Life film, which Lara and her cohorts use to travel to the Luna Temple. The vehicles are eventually destroyed by agents from the Shay Ling.