You could do a watercooling loop for just the graphics card, but would look weird and not really worth it. If you're gonna watercool, you may as well do the CPU and GPU in one loop. It can also get quite pricey, especially Danger Den stuff!
Custom set-up would consist of a pump, reservoir or some kind of fill port, CPU / GPU blocks, radiator with fans and of course tubing and coolant.
And to state the obvious, watercooling doesn't use water