What substrate do you have on the floor?
I've used washable incontinence pads for years. The boys I had were in a hutch in summer, and the small pads were a perfect size for the rooms in there, and the large ones do the inside cage, which the girls have always been in. We're now getting a 8 by 6 shed, which will be too large to cover in pads (which would need to be changed multiple times a week- I already do a ton of washing and don't need any more). The rabbits have pads in their shed, but since they're litter trained I just put them under the trays and in their snooze area, so I haven't had to cover it all, but with the guineas peeing wherever they like I would.
I'm thinking of putting lino down to protect the wood but then what?