A good portion of the air cooling cleaning still applies to you if you have water cooling, but there are still a few things you will have to take care to keep your water cooling running optimally. For starters, you need to recognize if you have a custom water cooling loop or an all in one system. An all in one system would be like an H50 or any other water cooler that you buy completely assembled from the manufacture. If you didn’t have to cut custom length hoses or fill it with water it is an all in one.
With both types of water cooling, you should remove the water block and clean off your old thermal paste and reapply fresh thermal paste. There are a few compounds that are made to help you clean up your thermal paste but I will be honest in my experience a dry cloth is actually really good at cleaning off the main portion off your CPU and heatsink, I then follow up with a dab of rubbing alcohol to make sure it is perfectly clean.
With your CPU and water block all cleaned up you just need to reapply thermal paste and reinstall it back onto your CPU. Follow your water block’s/water cooling’s instructions for the installation and for how much thermal paste I would recommend checking out the following articles for a little information HERE and HERE. If you need to pick up thermal paste for this project I would highly recommend Noctua’s NT-H1 thermal paste. A lot of people won’t use anything but Artic Silver but my experience with Noctua’s thermal paste has been great over the years. Not only does it not require setup or burn in time, it is also not electrically conductive. I don’t think I need to explain why that can be important.
With both custom and all in one water cooling kits you should pull your radiator fans off and clean out the radiator. With my wife’s PC for example, the cats love to play on top of it and their hair builds up on/in the radiator blocking the airflow if I don’t stay on top of it. Cleaning is just like cleaning your heatsink. You can wipe up anything on top and blow everything else out. While you are doing this be sure to clean the fans from both sides as well.
If you have an all in one kit, you should be all set. People with custom water cooling have one more step to take care of. With custom water cooling you should flush out your coolant around twice a year if possible, but worse case hitting it before every summer is a good idea. Every system install is completely different, so I’m not going to go into specifics on how to drain your system. For me, I drain everything I can and refill the system with distilled water and run it for a little while to clean everything out. A few coolant manufactures are now selling cleaning kits for this as well. I normally flush it a few times to make sure all of the old coolant is gone then I refill with new coolant of my preference. You can use distilled water by itself or with additives or go with a full coolant if you would like. It is important to never use tap or drinking water in your system, even when flushing because it can cause corrosion.
The reason we have to flush everything out is because even with additives you will eventually start to get bacteria growth inside of your coolant system. If left unchecked it will block the cooling passages in your water block and radiator, lowering the cooling performance. So don’t put it off, trust me cleaning that out of your system is much harder than a flush. With everything back together be sure to recheck for leaks and air bubbles in the lines. Last but not least, be sure to recheck the coolant level after running the system for a few days to top things off.