Even with water-cooling, you still have a pump that spins and creates noise. Those systems have reduced noise but not eliminate it. Read up on the chipset your mainboard uses, chances are you can remove the fans and be just fine as long as you're not overclocking. You can also use external harddrives in those acoustically sealed cases. Or for that matter, just put your computer under your desk/workstation/whatever, and surround it with acoustical foam attached to MDF.
There's all kinds of ways to deal with computer noise problems. I've seen all kinds of creative things.