some random ideas (do I have any other sort of idea?)
I have trouble shaking my deep-ones imagry so I see a lot of sort of decayed, subservient, alien, cult type religious stuff. YMMV.
[the problem with some of this is that it's sort of internal cultural stuff... it's kind of tricky to show off deep internal emotions of bit characters in a RPG]
biology influences mindset
*no family structure with a paired male & female. eggs are kept in communal areas. weird mating rituals are a must.... males fight in ritual combat for the right to "donate" to the next generation.
*so there are no families as we think of them and there is little incentive for a K-t to teach another K-t anything. An individual is always alone within K-t society
*these eggs are all kept together in big clumps and their keepers "sing" to them. K-t remember what they've heard after they've hatched. In effect an egg group is born with a genetic memory and common heritage (thus making them relatively easy to brainwash and control).
*most K-t learn very little after they have hatched, their rulers encourage this tendancy to keep them pliable and controlable. they've never been to a "school" most can't read, and have never learned anything. they aren't oriented toward aquiring new information.
a culture based rooted in fear. basically unlike most societies K-t don't think of themselves as being great and powerful
*. they know they're weaker and slower and dumber than the things that live around them. they are lucky to be living in a "free" city and not being slaves to the drow/abolith/mind flayers/whoever. -- kind of like the weak-minded Gollum's attitude in the two towers.
I like the idea that thousands of K-t tadpoles hatch in these big pits but only a few survive. The rest are fed to some kind of holy creature. The few that do survive to grow up remember the terrible screams of those that didn't make it and are forever marked by this deep seated fear-bordering-on-paranoia.
* =
I think just about every group in the real world and 95% of races in D&D are convinced that they are, for some reason, superior. So I think this would make an interesting change.
I also like the idea of their society being sort of like america during the red scare with this giant K-t preist-god stirring them up about the Aboliths who are lurking out of sight always ready to control them. You know the priests are always looking for Aboleth-slaves and race-traitors who want to sell their race back into slaver.
"An abolith mind-slave can't be reasoned with. It's obsessed with enslaving other Kua-toa and bringing them back to it's masters. You're quivering, Klib-ribt, are you... hiding something from me?"
Social structure
I see a few ways the society could be broken up
1. chaotic -- there is no social structure, per se. Individuals are just forced to do things by those who are more powerful
2. born into a caste -- different K-t "egg clumps" are sung to in different ways by the breeders.... movement through castes is unheard of (like the movie Antz without the happy ending). castes have a sort of compraderie and are arranged in a heirarchical manner (priests at the top, then warriors, pesants etc.)
3. egg-families --- K-t are organized into a clan-type structure. each clan has it's own breeders, rulers, warriors, priests, etc. The clans have a complex and shifting relationship with each other.
Within the clan you have different clutches (K-t who hatched from the same clump of eggs) who are all the same age and become a powergroup within a given clan. Kind of like people who entered a big company at the same time together (if you're familiar with that kind of environment.
4. clutch-brothers, the smaller egg-groups (your egg-brothers and sisters) are the major forces within society. Basically it's a society composed of many many 20-30 individual groups. Very chaotic, very tribal.
5. (This is probably the oddest, and the one that's most saterical of the real world). The K-ts are divided into different groups based on physical characteristics like skin patter. Some K-ts have little freckle like spots, others have larger patches, or stripe type vertical markings or what have you. These patterns appear more or less randomly and shortly after hatching the egg-groups break (or are broken) apart and the K-ts live with those of similar patterns.
city layout stuff
*I like the tides idea a lot, but instead of regular tides I would think about making it more complex (almost to the point that an outsider just won't understand the cycle at all). As different chambers build up above the city and on the surface at different rates you can have some extreme and chaotic tidal movements. Maybe the Kua-toa control these and have crude 'dam' type structures. Or maybe this is like their weather and periodically powerful violent current surge through and destroy buidlings and people. (this would help feed the fear/paranoia ethos I mentioned earlier if you go that route).
*GARBAGE Collection. I love the idea that there are a bunch of K-t who just hang out where the water flows and pick up garbage the flows down from the surface. They trade extensively and may have something neat (that they don't know is powerful, useful or interesting).
*definitely use the escape artist stuff, especially in structures built to be defensible
*I think you could do a lot with their vision and style of movement. A leader always wants people he doesn't trust to sit to his side so he can see them clearly. Furthermore if they try to do anything he can leap forward (and away) easily.
*the K-t cohort seems to have a very jumping oriented combat style. I could see concepts like "running away" or "standing your ground" as being completely foreign to them. Fighting properly involves a lot of movement, gaining the high ground and jumping at someone, etc.
*to continue with the vision thing, they probably don't like long stretches of hallway (because they can't see far forward well) and are extremely comfortable with hair pin turns and corridors that turn so much that they almost double back.
*no stairs. lots of ledges for jumping, domiciles (and buildings in general) are probably built on a much more vertical type of mindset. holes in the ceiling instead of stairs (croak before jumping of course)
*fast moving jets of water take messengers and people in a hurry through tight tunnels and let them get around the city quickly. (just don't bump the walls...

)
*art or writing that is set up for people who can't see directly in front of them (a book which is like a circle with a hole in it. You stick your head partway in and each word in a sentence is on the far side of from the prior. (OK that probably doesn't make sense but I'm flagging a bit here). basically you alternate reading each side of the reading-object word-by-word. In addition to being easy and natural for a K-t it's tough for a humanoid to easily do (since you would have to keep moving your head around inside to see every word clearly).
*If their vision is permenently bubble-eyed a lot of their art and scuplture is probably similar. (re-orienting their heads allows them vistas of perspective that other species can't experience or appriciate).
little bits
*jelly fish defenders, I'm actually imagining more like squid who can squirt along really quickly but which are translucent and have stingers. I like the idea of something that can move 200 once every few rounds.
*instead of physical barriers (like seaweed) for doors (which would flow around in the currents) maybe they have some kind of bubble-jets in front of entry ways of buildings to obscure sight
*weird religious moaning echoes throughout the water all the time. (creepy or dumb depending on how good the description is)
*water in certain chambers/areas is laced with somthing poisonous to non-Kua-toa
Ok. So they're immune to posion, I didn't have the mon man at work. So this is pretty reasonable
*a complex which is a variety of submerged & partially submerged and non-submerged rooms. The air is extremely poisonous; Kuo-toa know to stay underwater in these rooms but surface invaders might not figure out.good probably as an outer area threatened by drow.
I still like idea but since they're totally immune to poison they've probably just poisoned or tainted everything they could without worrying about having safe entry or exit areas.
*a balista that people or messages are attached to and then fired through the water (an alternative to the water jet's system).
What kind of mounts do K-t use?
I would tend toward giant frogs or snails (for carrying really heavy loads up veritcal surfaces).
I'm tapped out (and it's a three day vacation here!). Hope the rambling was of use or else set off other people's idea machines.
have a good weekend y'all
(times being what they are it's tough but anyway)
edits = some particularly egregious sentence fragments, html.