What would be my affiliation if I'm a Masters student? The question title pretty much says it all. I'm now a graduate student pursuing my Masters degree. Will the university I'm enrolled in be my affiliation when writing a paper?
Yes. 

And be sure to get it in there before you graduate. Though if you are not moving straight to another uni and plan on publishing more, if you talk to your prof they might hook you up with "affiliate" status. This means no money or much of anything else other than the ability to claim affiliation.