4 pin fans are PWM controlled fans. three pin fans are DC controlled fans.
Your motherboard expects a DC control for the CPU fan since it has a 3 pin connector. Most PWM fans, though, will operate on a DC control so go ahead and use it. The connectors are keyed (there's a plastic flag on the motherboard header that will slip between two tabs on the fan connector to locate it) so they will install correctly whether 3 pin or 4.
But it's also likely the motherboard will drive it with a constant +12V though with no adjustments for any other voltage output. That's the case with my Asus board, if that's the case with yours many coolers come with a 'quiet' adapter that drops voltage for that situation. You can also attach it to a case fan header if they allow adjustment of the DC voltage to control fan speed.
BTW...a 3 pin, constant +12V output header is correct for a liquid cooling pump since they're supposed to operate at full speed all the time.