Help on how mobos control fans

[MDXX]

So i bought a watercooler, makes an annoying noise when fans are going. (i have sensitive ears due to tinnitus -_-) So i was wondering, does just plugging the fan pins into mobo headers just cause it to run at full speed? Do i need some fan controller to control them? Or can i do it through some program or motherboard? I havnt done a fan profile before, so i could use some help thanks

 

[Ecolouge]

You will not want to adjust the speed of the water cooler pump, so if your fans on your radiator are plugged into to CPU fan slot...you should be able to adjust them in your BIOS or with an application.

 

[corroded]

the headers are full speed, except the CPU fan. There are fan speed controllers out there, I used to run one. My current case has fans w/ 3 speeds on them.