Before I go on, this is not a suggestion for a "wading under-water" sort of water-themed levels, but rather "heavy drizzle" sort-of levels. Just try to keep that in mind as I outline my suggestion.

General Area Theme
The main variable themes evident throughout will be the amount of puddles and the volume of the background noise - which shall be the sound of a rainstorm. The farther down the depths you descend, the more widespread the puddles shall be, and the rainstorm shall eventually turn from being the background music to the foreground.
The tiles themselves will be as they are near the higher stratum, but the deeper you go, the more of them shall be replaced by the "soiled" tiles; and by "soiled" I mean mossy.

Unique Features.
The feature which I have in mind is there being puddles everywhere, as I said before. The code, I imagine, would run something like how your footsteps change sound depending on where you step, and the effect for the water rippling can be modified from the files already in the 'water' file; just replace the overlaid water .png with another one if the Knight steps in it.
Another feature could be how the fountain effects could be re-used to imitate waling behind/through a waterfall. Of course this would have to be somewhere near the top levels since it is relatively placid.

Levels

Level 1: Gazing into the Surface

This level involves a non-strenuous walk, with the appropriate amount of rewards, through a lush wonderland of sunshine and - why the hell not? - have a group of Mewkats floating around on the top of a building just to show how peaceful it is. Overall, the ambience should be comparable to Treasure Vaults, just with a bit more monsters. Only near the end should the first couple of puddles and 'soiled' column and walls appear.

Level 2: Splashing the Surface

This is where the first unique enemy comes into play; the Pseudo-Hydro. The whole of this level is similar to the first, except that the spots of combat in bright areas are broken by long stretches of walking though a set of puddles surrounded spoiled tiles; and within the puddles lie a few Pseudo-Hydro. After the knights have gone through these stretches and gotten near the exit elevator, as they descend, instead of hearing the normal, triumphant music, they'll hear the sound of metal creaking and water dripping.
The rainstorm in the background will come to the fore every-time they pass through the hallways full of puddles.

Level 3: Lost in the Depths

This shall be where all pretence at this being a non-sinister area is gone and every tile and column and wall is spoiled. There are Pseudo-Hydros everywhere, but with these enemies becoming more commonplace, so arises a way to defeat them. Throwing Embers basically dries up the puddles and these enemies as well.
The embers are introduced before the 1st OR 2nd set of puddles/Pseudo-Hydros by a sign saying "It's not safe to wander these liquid depths. Destroy the water with these balls of fire.".
By now, the rainstorm has become insistently loud, though the battle music and the like is still able to drown it it out.

Level 4: Reaching the Bottom

This is where the sound of rain and thunder now drowns out everything else, except for the quiet din of battle, and a heavy rain filter is now put into place. Whilst there are puddles all over the place, the amount of embers is worryingly small and distant from each other.
After finally getting through this, the Knights then enter a large circular arena. Within this arena there exist a hole which is approximately a quarter the radius of the entire arena's radius. At each point of the compass, there exists 4 respawning embers, dotted around the outside of the hole. After standing on the party button near the bottom, the Knights then fight the Liquidine.
After defeating the Liquidine, the Knights can then enter onto the exit elevator, which is surprisingly... white. The Recon Module for this is written halfway, before it then cuts to "OVERWRITTEN The Shadows take many forms."

Enemies

• Pseudo-Hydro: These are enemies which look the same as Puddles from a distance, but get close enough and a face - which curiously resembles a Grimalkin's face with a water texture - will pop out and take a bite out of you. They don't appear at all in the first level, but will then start randomly replacing the puddles in all the levels thereafter, and in the final level every puddles is a Pseudo-Hydro. They, along with Puddles can only be destroyed by throwing embers at them, this will cause the puddles to evaporate and the Pseudo-Hydros to scream out before evaporating.
• Slubes: These are basically water-textured Jellies. Nothing more, nothing less. Their only purpose is to enhance the watery feeling of the level(s). In that sense, their decoration.
• Liquidine: The Liquidine is a big square lump of brackish water, so dark that you can't even see through it. At the beginning of the battle the Liquidine shall rise up and fire a volley of shots at the Knights.
  After this, it shall then summon two waves of monsters before rising up to attack the knights directly. It's attack involve a mortar-style blob of water, and a Jelly-style slap for any knights who loiter for too long near it.
  The only way to hurt it is to throw the embers located so thoughtfully around the center. After throwing enough the Liquidine will submerge and begin the next wave, this time throwing out water-mortars every so often.
  After that wave is gone, the monster will rise once again, except this time it will now let out waves of projectiles in a 360-degree arc. Hope your away from the center when that happens. It will also now start spawning Slubes every so often, regardless of the phase.
  After another final couple of waves the monster now pops back up once more, except it does so with a fresh wave of enemies! This is also its last phase, defeating it now will result in its death.

Notes
This whole thing is intended to be glut of concepts about how water levels can be handed. As you can see here there are levels, enemies, bosses and environmental stuff and various other ideas.
I do not intend for this to be turned into a legitimate set of levels, but rather the first three ones contain ways of showing how Water effects can be used within a level. The last level is just because.