Just installed Water Cooled CPU set up.

maybe your CPU fan isnt working try installing a new one or check the cable of the cpu fan if it is loose.

I am wondering if I have to change where the fan connection goes, as of right now it is connected to a switch that will allow me to turn the fan speen down as well as turn the lights off, maybe I need to connect it directly to the mother board.

@Max the fan is on, I took the front end of the case off to verify that lastnight before I posted.

You definately need to attatch the Heat Sink FAN (water coolers still have fans) to the motherboard. Look for 3 pins sticking out of the motherboard, somewhere near to the CPU socket. If it's not plugged in there then the motherboard will think there is no cooling for the CPU and wont boot, I would have thought.

The fan speed controller on the case is for CASE FANS, which are a different thing altogether.

correct, somewhere close to your cpu socket youll see the cpu_fan plug in. you should have a pump that uses the same 3 pin set up, could you plug your pump in and still keep your fan control?

One little tidbit when you water cool. Not only does the CPU fan actively move air across the, but also the power supply MOSFETs on the mainboard that supply stable current to the CPU. These MOSFETs are arranged around the CPU and are designed to work at higher temperatures, but still are reliant on the CPU fan moving air across them. So make sure you have some sort of active cooling still happening in your case, albeit a large, slow-spinning case fan works better for this.

Also, you can always just disable the sensor in BIOS if you know you do not really need it. Some water pumps also have a connector that allows the pump to report its RPM to the CPU sensor so the mainboard can monitor the pump activity (serves about the same purpose allowing the computer to warn you when the pump is not running).

Yeah, I found the connection on the motherboard, don't know why I plugged that fan into to the speed controls.....It is working awesome now, just need to find a program to see the core temp and clocking speed when logged into windows.

I haven't thought of that but I may check it out later, problem is I don't think that having an adjustable fan for the processor cooling system wouldn't do to good.