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You have the waterblock on the CPU, which transfers the heat to the liquid which then goes to the radiator to cool down. Then the cold water runs back to the waterblock and pick up heat again.

Now depending on what you are talking about, custom or All-in-One (AiO) the answer might vary both in how they work and how they peform. But generally what matters is the size of the radiator when it comes to performance. 

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Water cooling isn't as special as it sounds. It looks cool, but it's something very basic.

 

You have the resorvair in which there is water. Under that resorvair you usually have pump that is pushing water around. Then you have connection from pump to CPU waterblock. That waterblock is one huge heatsink. One side of that waterblock is contacting CPU, and on another side of that metal is water flowing around. That metal (nicekl or copper) is heated by CPU, but water inside the loop is cooling it down.  If there would be no water flowing around, temperatures would go up and up and up, untill it would overheat.

Water goes from CPU waterblock to radiator, which is a huge heatsink on it's own. Water is flowing in pipes, that have aluminum fins on the outside. Those fins are working as heatsink. You also have fans on that radiator, because those fins get hot from all the hot water inside. That's why fans are blowing air trough radiaot (fins) and cooling them down. Efectitly cooling down water inside that loop. And from radiator water gets back to resorvair.

 

Sorry for bad english and not very decent explanation, but that's the basic of it. If you want more informations just look some tutorials on youtube.

 

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The process that goes on in a water cooling loop is literally the same as what goes on with a standard CPU/GPU cooler. The only difference is that the water takes on the heat/energy instead of the heat pipes which allows you to place the cooler (radiator) elsewhere, often allowing for much larger coolers.

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