If you have seen my previous questions then this may make better sense. If you put an insanely powerful superconducter on the outside layer of a ROV that is underwater, would it form an outer layer around it of near nothingness, if the water is only H2O? What I mean is, since water is a polar molecule and in the scenario I am using no other molecule is in the water, shouldn't it make a smooth layer of nothing around it? And if this is feasible, would it keep neutral buoyancy?
OK - if you want to repel water from the surface of your device, you may have better luck finding a hydrophobic coating for your device, a la: ORNL scientists discover superhydrophobic coating
Superconductors themselves are perfect diamagnets, which is why they are able to expel magnetic fields from the bulk, with different levels of magnetic field support for different superconductor classes and applied fields. Type II superconductors are capable of producing strong magnetic fields in a mixed state (see MRI, and the superconducting magnets at RHIC/LHC), but bear in mind that these operate at extremely low temperatures using liquid helium which is expensive. The critical fields for high temperature superconductors like cuprates are lower, which is why applications requiring strong magnetic fields are still using the helium based versions. Unfortunately, there is no low cost, high temperature superconductor, and in no way is this due to lack of effort by thousands of people.
For the actual question about repelling the water, if you can get a superconductor that produces a strong enough magnetic field and you can get the field orientation issues sorted, then sure, you could use a superconductor to repel water, but this is due to the diamagnetism of the water, and not the polar character of the water. There are ton of youtube videos demonstrating this phenomena.
Further, I don't know that I understand what you mean by "keep neutral buoyancy", but since buoyancy is driven by the balance of an objects density and the density of the suspending liquid, I suspect that the normal rules of buoyancy would still apply, but with some modification to what one would consider to be the boundary of the suspended object extended out the the finite spatial extent of the magnetic field.
Finally, an event where your superconducting magnet suddenly became non-superconducting (see LHC magnet quench of 2008) might blow your device up, but I'm not sure what would be the effect of dumping compressed cryogens into the ocean at any depth. Maybe it would become a floating block of ice? Just something to consider.
Water is weakly diamagnetic so is aligned by a strong magnetic field.