I have no idea how much you'll understand these rough notes, but here's what your latest map inspired.
This was originally a dwarven temple dedicated to Ares. It is located in a remote passage of Moria because worship of Ares was never acceptable.
Quest ideas
-old artifacts of war that draw on the power of Ares rest here. The Mercenaries Guild will hire the PCs to retrieve these for Ares. Another Guild might hire the PCs to stop the Mercenaries Guild.
-Mindflayers lair here. One of their plans is to enslave the city's royalty. The Dragon's Guild wants them stopped. The Cult of Vecna wants to help them
-The mindflayers have also begun infiltrating the Library of Hephaestus. Aphrodite has noticed some odd behavior and asks the players to investigate.
- A unique beast has been spotted and might lair here. The Circle of Sobek is always eager to enlarge its zoo (or museum, if the players are lousy trappers).
Water.
The temple is flooded. Water flows from area 30 through the shattered door of area 17, with moderate current throughout main floor and open doors, with a strong current from the south end of area 18 through the hall to area 8, becoming a torrent through to area 9 and the pit traps in area 5 (and the ultimate danger of being swept in). It is knee high throughout except Areas 1-5 because the doors to those areas are sealed, the pit traps in area 5 magically destroy water (and people who fall in!) and area 5c is dammed.
The stairs in area 18 and the level below are permanently flooded.
Creatures
Areas 1-5 (and up the stairs) is barricaded by mindflayers who use this as an isolated, remote base. The doors into this section have all been magically sealed, barred and magically locked and trapped. Area 5 is always well guarded, although the guards try to keep out of sight, so no one knows they are there.
Another monstrous faction uses Areas 23-27 as an outpost. They've built wooden platforms throughout to keep their beds and belongings dry, but slog through the water, living like Venice in a flood.
There is a 50% chance that areas 10-14 are occupied by another monstrous faction. This can result in the same faction as above, and thus this outpost is simply bigger. For different factions, roll 1d6: 1-2: factions are indifferent to each other; 3-4) they are foes; 5-6) they are allies.
Wandering monsters are mostly amphibious beasts.
Notes
The doors to areas 7, 9, 15 and 21 and 28 are sealed from water and have been left untouched by the mindflayers, various factions and wandering monsters, meaning ancient treasures might be found here. Area 9, close to the mindflayers' disintegration pits, should hold the most valuable. The secret door to area 21 suggests another valuable treasure ought to be there. The secret doors to 28 make for a path to the mindflayers' lair that they are unaware of, making ambushing them or sneaking in possible.