Im thinking about working out underwater...

That sure seems like you'd be removing most of the "bodyweight" idea... are you wondering about water workouts from a rehabilitation perspective?  What's your motivation? 

Actually this could be quite interesting if you were using the TRX completely underwater, with scuba gear. Working out underwater would increase the amount of resistance because water is 1,000 times more dense than air and moving through it it more difficult and requires much more efficiency than moving on land.

With the proper gear, one could do a TRX workout underwater.

 While it is certainly true that water is 1000 times more dense than air, there is one major drawback to consider... 

It's bouyancy creates a weightless environment

To counter act the bouncy and weightlessness you could use scuba gear to keep your self on the bottom. You would have to watch to make sure you don't get your cables and crossed or twisted, that would be bad.