There's some good underwater dungeons in the skulls &shackles AP. 1st and 2ndthe chapters especially. You coulx buy the pdfs and adapt them.
Did you play Ocarina of Time?
What level are the PCs? What classes/races? What abilities do they have? Hard to suggest useful encounters without some idea of who's going through them.
That said:
Read the environment rules carefulky and throughly, because they will come up a lot. In particular, not weapon effects, and realize that underwater creatures will probably mostly use spears or other piercing weapons.
How are the players breathing? Can the enemy sunder their breath masks or dispel their water breathing? What happens if they do? Will the players be able to get back to the surface in time? Smart enemies, and aboleths are nothing if not brainy, will certainly think of this tactic.
A few illusions, particularly walls concealing secret entrances, will be interesting. Expect the locals to know their terrain very well, and remember that anyone with a swim speed can effectively fly through the area. PCs may not expect enemies to swim out of an illusion-covered hole inthe ceiling, or to emerge from out of a kelp bed.
An octopus with the ability to flood the water with black ink can be very annoying, as can grappling vines or other hindering traps. Pits won't be around -- they're not a threat to swimming creatures.
Some of the aboleth a servants may be dominated, charmed, or otherwise unwilling slaves. If the party can rescue them they may gain a valuable ally -- at the bare least, someone who knows some answers and locations. Of course, the aboleth could have lied to its servants.
A dedicated temple might have undead and/or a hallow spell with some interesting effects attached to it. Or, if its been taken over by a godless aboleth, maybe the ghost of the last priest is still hanging around, and might be an ally to the PCs. Or an enemy -- maybe it wants to use the Pcs to kill the aboleth, but then wants to kill them for desecrating its temple...
The dwarf wizard is high enough level to cast water breathing, and if I were him I'd also prepare an emergency scroll or two of it as well. If he doesn't know the spell maybe the merfolk can teach him or something.
Now if we assume aboleth as the BBEG, several skum servants, maybe with class levels, and a few pet sharks, octopus, or something else, that gives you a number of encounters. PCs might have to be careful not to let the enemy swarm them. A silence spell coul dodge very handy for stealth, but then how do the PCs communicate?
Traps: Anything that either raises an alarm (bells?) or holds intruders in place for the wandering patrol of skum to find (ropes? Chain nets? Animated objects? An assassin vine reflavoured as evil kelp?). It's a little low for the CR, but assassin kelp makes a nice sentry, and you could have several scattered around the outside, so the PCs only have to meet one of them, unless they run away in another direction.
Puzzles: not so much water raising as water lowering. Maybe there's something useful in a sealed-off chamber that will be destroyed if water gets into it. A map or spellbook printed on fragile paper, a valuable.drow artwork composed of spider silk, etc. maybe three stone statues have to be put back in the right places to lower the water -- be simple, otherwise the PCs will never figure it out. Unfortunately there ate four statues, and if they put the wrong one in it animates and attacks them. Various knowledge checks, or carvings onthe statues, or whatever, can give the Pcs clues if they think to look.
Possibly levers in some places with. Little puzzles attached. If you solve the puzzle and pull the lever, it lowers, or raises, a steel gate that blocks off part of the temple. If the PCs are clever they can use these to split up their foes and real with them separately. Or they can unleash something kept in a cage and have to fight it if theyre not careful. If they're not careful their enemies can trip the gates and split them up, or trap them in a dead-end corridor with some undead or something -- a few lacedon scavengers, maybe? Or a scrag? (Marine troll. Very dangerous underwater, but if the PCs can befriend it or break the aboleth a control, it would be a powerful ally. Or course, the merfolk might not like it very much if the troll were freed.)