If you're communicating the fact that the books and things can't be removed from the water without damaging them to the players, you could play into that with the loot. Things like powerful scrolls or even entire spellbooks, for example - but if they're removed from the water, they quickly become useless. Let your party's wizard figure out how they're going to copy that spellbook when they have to do it underwater. Maybe they'll keep the scrolls in bottles filled with water until they need them.
You could also include traps specific to that area. Think like, for example, a magical barrier that traps anyone who steals the books in that section - and underwater - until they put the things they took back. Maybe it malfunctions, and doesn't de-activate.
It's hard to give specifics, because you didn't mention what level the party is expected to be when they get to this section.