I had a problem with a wet and muddy coop floor at the beginning of winter. My coop floor is part plastic and part natural earth (= it sits straight on the ground) and I had rainwater soaking through from where the walls meet the ground. After unsuccessfully trying twigs and shredded palm leaves as litter, I finally settled for a good layer of sand. That has helped keeping the coop (and the chickens) a lot more dry and clean. Maybe a layer of sand underneath your litter might help.
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