Mixed water and air environments could indeed be quite dangerous in microgravity. But an all-water environment should be possible. For a human to experience sustained microgravity already requires a breathing apparatus; often this is habitat- or capsule-sized, but personal units exist as well.
Several people have commented on the challenge of moving between all-air and all-water habitat volumes by an air lock.
Existing practice for cleaning up liquid spills is the use of a vacuum hose (likely venting to space, which would be wasteful of mass at air lock volume) and towels. A chamber could be designed to blow in air and pump out water (initially through vents, later via a handheld hose for catching globs) and separate the suctioned air and water via a centrifugal dryer and possibly a refrigeration-type dehumidifier at the final stages.
However, there's also another Earth technology which could be quite applicable to initial separation: air bladder water tanks. An astronaut wanting to move from the air environment into the water one would enter the airlock, don the breathing apparatus and zip themselves into a flexible bladder connected to the water side door. The air pressure in the surrounding chamber would then be slightly raised, while that inside the bladder lowered, effectively "vacuum packing" the astronaut (but only weakly, so that they can continue to breathe). Once most of the air has been removed from the bladder, the external pressure is slightly lowered and water pumped into the bladder. They are then free to open the water door, and enter the water environment.
To exit the water environment, they pass through the door into the bladder and close the door behind them. The external pressure is again slightly increased, and the water pumped out. Once most of the water has been removed from the bladder, they unzip, and use the previously mentioned recirculating blower, suction hose, and towels to clean up.
Finally, while orientation could indeed be a challenge, it is not likely to be more challenging in a microgravity water environment than it already is in a microgravity air one.
If there is a unique danger, it would be with things like water aspiration resulting from partial mis-operation of the breathing apparatus. Things an Earth-bound diver can do will probably not be safe. It's quite possible the astronaut should effectively wear a drysuit during their time in the water habitat.