First, I agree, more info needed. Especially exactly what water cooler system - maker and exact model number. Then it also helps a lot if you tell us exactly what mobo you have, too. The reason is that makers of different AIO systems have used different control strategies, and that affects what connections are to be made. Thus, it usually is a REALLY good idea to follow the instructions of the AIO maker.
Many AIO systems intend that the PUMP unit run full speed all the time, and hence that item needs a constant +12 VDC power supply. Normally one does NOT try to set a different speed, and certainly not a speed that varies all the time as a fan would. These systems do all control of cooling the CPU (guided by a temperature sensor built into the CPU chip) by changing the speed of the rad FANS only. Trying to change both the fan and pump speeds makes for a very difficult and confused control algorithm.
You often see a cable from the PUMP to the CPU_FAN header that ends in a THREE-pin (well, hole) fan connector. This design is using a quirk of the new 4-pin fan system design. In the older 3-pin fan system, the pins are #1 Ground, #2 +VDC supply, and #3 Speed Signal. The voltage on Pin #2 is varied from +12 VDC max down to about +5 VDC min (so it does not stall), and speed is controlled by varying this voltage supply. In the New 4-pin PWM system, that Voltage on Pin #2 is ALWAYS +12 VDC, and there is a new PWM signal supplied to the fan on Pin #4. Within the fan there is a small chip that uses the PWM signal to modify flow of current from the constant +12 VDC supply through the windings to change motor speed. BUT if you plug into that 4-pin CPU_FAN header that is doing things the new PWM way with a 3-pin connection, the device (in this case, the AIO PUMP) receives a constant +12 VDC from Pin #2 and NO PWM signal from Pin #4 that is not being used. So it runs full speed, and that is what the AIO system designers want to happen. So leaving the CPU_FAN header set to the new PWM Mode is just the RIGHT setting. Alternatively you could set that header to always send its fan (well, pump, really) a signal to run full speed. But the one option you generally do NOT want on that header is to set it to use the older Voltage Control Mode and then vary the voltage on Pin #2 to change the pump speed. That is NOT what the designers intended, in general.
There is a second important function of the CPU_FAN header: detection of FAILURE of the CPU cooler. This is done by checking the speed signal coming back to the header from the fan on Pin #3. If there is NO speed (or, in some cases, a speed slower than a set limit) that triggers an alarm and may (depends on the mobo design) cause complete shut-down even before the CPU's internal temp sensor can detect a high temp. Now, when you are using an AIO system there are TWO components required for cooling - the pump and the rad fan(s). Of these, the pump is more critical becasue its failure means virtually NO heat removed from the CPU. Failure of one (or even all) of the rad fans definitelty reduces cooling too much, but does not result in NO cooling. So, it usually is best to connect the PUMP unit to the CPU_FAN header and let that failure detection system do its job. The you need to follow the instructions of the system makers for how to connect and control the rad fans.
There are many mobos on the market now that include special headers on the mobo like CPU_OPT, W_PUMP, etc. that can be set to feed the full 12 VDC supply to the pump, and can monitor the pump motor speed for failure. Some do not make it clear completely in the manual that they are doing all these functions. And of course, many AIO system makers design for the mobos that do NOT have these extra headers on them. So IF you have extra special-purpose headers like that, you need to understand what they offer and how you can use them.
There are some AIO systems designed for a different control strategy. Rather than connecting their pump and fans to mobo headers to let the mobo do its normal controls, these systems take over some of these functions themselves. Typically the PUMP is plugged into the CPU_FAN header to use that failure detection system. But then the pump also has a connection to a PSU power output for power and a cable that plugs into a mobo USB2 header. Then you must download and install a software utility that actually does the control work. This tool uses the USB2 connection to communicate with the pump module which also contains the fan control system. So pump speed is monitored by the CPU_FAN header for failure, but pump power and fan power comes directly from the PSU; control of rad fan speed (sometimes also pump speed) is done entirely by the software utility supplied. Since this type of system (and several others) differs quite a bit from the simpler "let-the-mobo-do-it" systems, it IS important that you read and follow the instructions that come with YOUR AIO system.
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