The idea of this level is there's a big ring-shaped central water-filled area—the namesake aquifer—in the middle of which is an area made of several concentric rooms, which are your eventual destination. Around the aquifer is a series of areas you'll be visiting in a counterclockwise order.
You begin in a good-size room with decorations, the exit of which is the Yellow Door. Nearby is a stone door which will be open later. Also nearby is a window looking out into the aquifer. You'll attract the attention of a couple of Iron Liches; try using your Firemace to fight them. You should also be able to reach many of the enemies in the inner area, through the window across the aquifer. After clearing out the enemies, step onto the platform where the Ethereal Crossbow and Arrows are. When you do, three doors into a small wood-paneled area nearby will open. Inside here is the Yellow Key, plus there are items in the compartments.
Open and go through the Yellow Door upstairs. In here is a long passage made of a series of undulating steps, ending at a large wooden door. There are two secret areas along this passage: in the flashing section, look to the side for a section of wall that has a decoration at the top. This is a hidden door to the first secret area. For the second, look further up the passage for another identical door. When you've collected the items inside, go through the wooden door at the end of the passage to the second room.
The second room looks like a big audience chamber and throne room. A window looks out into the aquifer, and opposite the entrance is the Green Door. Next to the window you'll find a small door, which goes to a bonus area. At the end of the meandering passage (watch out for the Weredragons) you'll come to a small ring-shaped passage filled with lava. Quickly run around to the far end of the passage, where you'll find a Phoenix Rod and a stash of Flame Orbs. (Tip: skip this for now if you have a full supply of Flame Orbs.)
Go up the steps to the thrones. When you step in front of the thrones, a door behind them will open, with enemies and the Green Key inside. When you pick up the Green Key, another area will open and you'll get a minor ambush. There are a bunch of Mace Spheres in this inner area.
Go through the Green Door and down to another smallish room, where there's a row of red pedestals and a window looking into a side room. The main route continues down. First, step onto any of the pedestals, and a door next to the window will open, leading into the side room, where there's a Dragon Claw. After you get it, continue downstairs to the third room.
The passage down will split, going left and right. On the wall ahead is a gold symbol: activate this for a hidden area with an item. Down in the third room, on each end there's a platform. On one is the Blue Key, on the other a teleporter. Another window looks out into the aquifer, and across from this is a long out-of-reach shelf with many items. You can only reach this with Wings of Wrath which you'll find later, so don't forget about it if you want the items. In the middle of the room is a low section of ceiling that—probably needless to say at this point in the game—is a crusher that activates when you walk under it. (But you can use this to kill enemies in the room.)
Collect the Blue Key. When you do, two areas on either side of the teleporter across the room will open, with enemies inside. After dealing with them, look in the opened areas (where the blue floor is), where you'll find a Map Scroll and another item. After getting them, take the teleporter, which goes to the inner area the aquifer surrounds.
You'll arrive here on top of a teleporter, which goes back to the third room. Around on the opposite side of the area (the south side, facing the room where you began the level) you'll find another identical teleporter, with Wings of Wrath on top of it. This teleporter takes you out into the aquifer itself. There are many, many items here, and this is also a great place to fly around. When you're done in here, look along the outer wall near the northeast corner for a small inset area. This is a door to a water-filled room; the teleporter in here goes back to where you began the level. When you return here, the stone door will be open. This is just a bonus area with a few items, plus a few enemies. When you go for the Mystic Urn a second room across from you will open, with a Firemace inside.
Back in the inner area, you'll find the Blue Door, inside which is a room with the exit portal. Watch out: there are two Iron Liches in here, and it's easy to get toasted by their fireball weapons, because of their close range. After you've seen everything, return here and enter the exit portal to resume your main mission.