The symptoms you are describing is often called 'cage aggression', rabbits can be very protective of THEIR space. It can take several forms, from growling to lunging to biting. It will generally decrease as the bunny gets more comfortable with you, but THEIR house is THEIRS, and until you are fully accepted as part of their warren, you may have issues.
First step in dealing with this issue, is to allow you to address housekeeping concerns in her space without causing conflict or stress. You should bunny proof particularly in out of the way areas. Ideally your bunny cage is on the floor, or has a ramp so she can get in and out of her space by herself. While she is out getting her daily exercise in the living room, you can clean her room and add hay, water & such. In some cases with very protective bunnies you may need to block her from getting back to her space, while you are working.
For a long term solution, it is all about spending time with your bunny. Her cage is her space so start by spending time together in a shared space. If you have not bunny proofed the entire area she can get to while out; use an exercise pen (x-pen) to fence off an area around her space, let her come out and get to know you. She is entering "your" space here, so she will go slower, be more hesitant and generally treat you as the alpha.
Depending on how much handling she had before you adopted her, she may snuggle right up to you for pets or it may take some time to get there. As the relationship between you grows, the whole cage aggression thing will decrease. Everybunny is a different individual so progress and outcome will very. I know one bunny that took more than a year to get past some sever issues (much worse than you describe here). My wife does a lot work with these kind of behavior issues, and most of the cases that are significant enough for special treatment can be addressed in 1 to 3 months.
We have a bunny named Tigger, who came to us to get his cage aggression treated. My wife later adopted him, because she fell in love; He does not have any remaining cage aggression, but he still growls.
In summary. By doing the cage cleaning while she is out, you will not aggravate the issue and will have a faster end to the behavior. The more time you can spend building a relationship with your bunny, the faster you will get past the behavior.
