If you connect the cpu cooler ( your water cooler) fan into the fan controller, you may get problem because the PC can't find the cooler fan on MB during boot, then the PC can't boot. And if your MB has the option to disable in the BIOS like warning cpu fan failure and you will be OK.
Hi, and thanks for your reply. The pump has a molex and a four pin CPU fan connecter. So I can power it from the fan controller and still plug it in to the motherboard. I guess I was more worried about powering a 12v pump from my 3pin fan controller.