Unless you either have a need for an ultra-silent computer (recording studio) or are a serious overclocker, I recommend against water cooling.
Water cooling adds a large number of additional things that can go wrong with your computer. The obvious is that "liquids and computers do not mix". And because it replaces conventional cooling systems, if a component does fail, you are much more likely to lose your CPU and other components.
I recently saw a desktop which had water cooling. The water pump failed, and within seconds the CPU was burned out. Once the water stops moving, the components heat up very fast. With this guy, he had a motherboard alarm go off saying excessive heat, and before he could turn it off his system blue screened and went off. His 4 month old Pentium D was now a small paperwright.
Just like anything else, I am not saying to not do it. But be aware of the risks, and of what you are doing when you decide on water cooling. And be prepared for failures that can cost you extra in replaceing parts.
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