You wouldn't need to water cool necessary, just identify the sources of noise.
Case Fans
CPU Fans
GPU Fans
Power Supply Fans
HDD
Are the main culprits. Not counting the CD/DVD Drive, since that's not on constantly. You could swap out the Case fans for something like the Gentle Typhoons, or the S-Flex 800RPMs, HDD silencers are easy to come by, there are pleanty of quiet (or even passive) CPU and GPU coolers around (namely the Scythe Zipang 2, AC Pro, HR-01 and the graphics coolers on offer. That leaves the main source of noise as the PSU, which is tricky if you have a noisy one to start with. I suppose with a hacksaw and a lot of patience you might be able to swap it out, but it's not the best solution since it's quite risky and you would void the warranty. If it bothers you that much though...