I'm going to ask my roommates gf to stop using my bathroom
What makes you uncomfortable with her using your bathroom?
I pay for this house and I've told her not to use it because she seems to be a big waster of water.
If the bathroom that your roommates girlfriend is using is the only bathroom in the home, it is rude to ask her to not use it. As long as your roommate pays his share of the bills, you shouldn't try to prevent his girlfriend from using the bathroom.
It's my house and I'm the one paying for it. I don't want her to waste the water and my money.
She is a guest in your home and it is not courteous to try and exile her from using the bathroom. If you feel that she's using an excessive amount of water, you should bring it up to your roommate in a polite way.