Nothing says a habitat must be on the absolute bottom of a body of water. In fact, because air is so buoyant, the real challenge is keeping them on the bottom. Any air filled structure when submerged behaves very much like a balloon. So, supposing you want your hab to 'hover' at a precise depth in a much deeper lake or part of the ocean. It can be carefully weighted to neutral buoyancy and then fitted with computers that micro manage a smaller ballast tank to keep it at the desired depth, or much more simply, you can just hold it down with a tether.
This one's not intended for animals, much too small. You'll notice it's partially flooded, this was to keep it submerged; the weight is not as yet sufficient. I'm going to either grow plants in it (short grass probably) or carve a very large circular moon pool in the bottom and use it as an RC submarine hangar. The little radio controlled Graupner microsub I showed off in earlier videos would then have someplace underwater that it can surface and 'park'. What might be neat in the future is to fit it with the electronics from one of those new short range wireless charging pads for cell phones, such that the little sub can charge in its undersea garage, and never have to surface again.
Incidentally, this "tethered balloon" habitat concept borrows from an actual undersea lab of very similar design, Jacques Rougerie's "Galathee" which could, by cable and winch, raise and lower itself like an elevator. This allowed it to also serve as a decompression chamber, or to observe specific levels of the water column.