The tiny water tanks that they live in on the USS Cerritos seem too small.Well, science is more aware of that now than when SeaQuest was made, and I think the public is more aware of it too.
I don't think it's enough room compared to a dedicated vessel like what we saw with the Xindi Aquatics.
I could see a future where the UFP has a special StarShip designed for Aquatic Animal life with a minor area with normal air for regular Bi-PaBs {Bi-(Pedal & Brachial)-oids} like us.
Sometimes, different species need to be amongst their own kind in StarShips that are designed for them if they plan on exploring the Stars with us.