Well everything will speed up when the computer gets put under more load.
CPU fan will speed up to keep CPU cool
GPU fans will speed up to keep GPU's cool
And PSU fans will speed up, again, to keep it cool
It could just be a combination of all components. Getting a noise-reducing case might be a better over-all purchase. Cooler Master sell a case called the SILENCIO which had some alright reviews. FRACTAL are also known for their quiet cases too.