Litter box

Hi, my name is Rebecca and I have a one and a half year old female lionhead. She is litter box trained or was and has a cage, but the door is left open. So recently my rabbit decided she no longer wanted to pee in her litter box all the time. I then moved the litter box into the center of the cage where she was peeing which fixed the problem for about a week. She has since gone to peeing by her water dish or even in her water dish. Any suggestions on how I can make her go back to peeing in her litter box fill time?

Number of issues and helpful tips:

1) Is she spayed?
2) Have you recently changed litter? Changed the room in any way? Altered her daily routine?
3) Some rabbits require retraining especially if you have recently given her more time out. Here, you may need to retrain, re limit space.
4)multiple litter boxes may help, and you can slowly take them away.

The cage is about 3' by 1' and she doesn't come out on her own. The litter box is cleaned twice a day and nothing has been changed, but she has not been spayed.

Perhaps you are cleaning it too often which confuses her as to where to go? I clean mine once daily but I have two rabbits, others on here go longer.

I agree with stevesmum.
I clean out my buns litter box probably every 2 days and that seems to be enough, when I was cleaning it too often my bun would have 'accidents' and I was sure it was because she couldn't smell where to go.

Not saying this is what's happening with your bun, but just thought I would add that