When you say a new mobo I'll take that as it's a store bought unit in a box. If this is the case it will come with a manual to assist with that end. It will explain all the details necessary to install. Read it first and simply reverse instructions to remove existing mobo. It's not that big of deal.
The water cooling loop will have to drained, remove a tube that will allow you to drain water without spilling onto components and if you're lucky it may even have a drain tube. If this water cooler is a closed loop like a HS50 etc it's even easier, just remove the water block from the CPU and set it off to the side if possible and at worst case remove entire system which is an all in one radiator with two lines permanently attached to the water block. A true loop will have either quick disconnects or barbs with tubing attached with clamps that can be removed.
When reinstalling water block use a quality thermal grease such as Arctic Silver 5 and you can find threads or make another post if your not sure on how to apply the grease. This is probably the most critical part. Never just slap the grease on, there is a proper way to do this.
Depending on the water cooler just reverse order of uninstall. If it is a true loop with barbs, take notice of the condition of the tubing as it may need replacing due to build up inside the tubing. If you have doubts, replace it. Fill with distilled water and either use a silver kill coil or PT Nuke. You'll need to unplug all power connector from mobo to prime and bleed air out of the system before just turning it on, than leave it run to check for leaks, this is very important.
These are the basic steps, if you need more info check in the water cooling threads for your current system and ask there. There are basically 2 ways it can go so it shouldn't be that hard to figure out which you're dealing with.
This thread might come in handy with most questions http://www.overclock.net/water-cooli...-rs-rx120.html
If I can help any further feel free to PM me or just ask in one of the other threads listed above.
Hope this is of some help, good luck!