Just wonder as Star Trek never been to a Under Water base where the inhabitants live under water? Never seen them land a shuttle underwater.

Guess the Under water Version of Star Trek would be Sea Trek. Star Fleet sure has Underwater special subs or whatever.

One episode of Voyager (Thirty Days) involved the Delta Flyer flying into a water world. They might be able to go underwater, but starships and standard shuttles weren't really designed for it. Starfleet probably has special craft designed for traversing liquid environments, such as the multi-purpose aqua-shuttle from Star Trek: The Animated Series.

Shuttles being able to go underwater is sounding a little too much like the puddle jumpers from Star Gate series.

He is right they have done that. In voyager.

I am not sure about true Underwater, but I would figure if a starship could enter a liquid environment in a Gas Giant Planet, actual underwater environments would not be too difficult. Again though, this would no doubt be a rare and not ideal condition, as Starships are designed for space and not underwater, so I would say it would not be the norm for any vessel.

-Futurama, "The Deep South"

It was stated Voyager could be modified, but for time they modded the flyer.
There's also Fluidic Space...

Jup, but i think ships like galaxy class diving into the sea and back launching again.. I think its too heavy?

ALL POWER TO THE ENGINES

I'M GIVING EVERYTHING SHES GOT SIRRR!