The Challenge Rooms introduce players to nanotech powers, allowing them to manipulate the water flooding the ship/city. Once again, according to a representative for developer Dark Energy Digital, these powers are not part of the first game, but are certain to be in the sequel, which is already in development and should be done in about a year.
If you ever played Psi-Ops: The Mindgate Conspiracy, you've got a pretty good primer on how Hydrophobia's powers will work. The main difference being that instead of the protagonist's mind manipulating objects, she manipulates the water. She'll push boxes around with the water, lifting them up in the air to help with obstacles or tossing them across the room at enemies. One of the cooler things we saw is when she lifts the water around an enemy, causing them to drown in a six-foot column of H2O they can't swim out of.
It's a shame that these powers won't be in the first Hydrophobia, but it's nice to see that players will have them in the Challenge Rooms and can look forward to using them in the sequel. It's an interesting test for the developer -- for those who become fans of the Challenge Rooms, they'll have higher expectations for the sequel if they've been playing with the powers for a year. Of course, the developer will get pretty good feedback of which powers the players think work well and which ones need tweaking for the in-development sequel.