Hay can become moldy. It might be better to reroute any water or put some temporary pallets in there. Pine shavings are better for bedding, but even those will become moldy with staying wet. Sand might be an option.
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My covered run is a muddy mess! I gathered a bunch of free pallets and laid them down and put plywood over them, then threw in a bunch of shavings and the girls had a great week spreading it around.
Seems like you are giving these girls a better life by far than they had. You are clearly a caring person.
What I see of commercially bought coops are usually skinny poles not flat boards, so might be worth consideration to avoid further issues. If you live in a warmer climate it seems less crucial of course.
Avoiding mud is helpful to prevent problems too. I put up a temporary run mid winter in a spot that had been getting too much foot traffic so was muddy. I've been throwing hay straw and wood shavings down as the mud starts to show, their feet might get a bit wet but not mud encased at least.
Good luck with your flock.
That's my goal as well but I didn't plan ahead so have limited materials available. I know wet hay can mold but I almost think that's less likely if you keep the dry materials coming regularly. I have nothing to support that opinion except years of cleaning hay up.My run is deep litter. If not for the deep litter, it would also be muddy. I have worked for 3 years to build up a nice thick layer, which is now about 6" deep in their winter sunroom area. Leaves, grass clippings, hay, garden debris, aged wood chips. I use the same bedding in my coop. Have never had issues with moldy hay. These materials eventually break down into a lovely black fragrant compost which I can harvest for my gardening.
The right blend makes sense. I have a little wood chips in there but they are fresh so only a bit, plus a good amount of shavings. I'm confident this will hold till spring.I think it's less likely to mold when mixed with other materials. In all of my years of putting hay in garden (35 years) coops (total of 10+ years) and run (3+ years), I've never had issue with mold. Every fall, I take the truck during leaf season and go through neighborhoods "poaching" bagged leaves from curbs in the "old" neighborhoods where the yards are loaded with mature trees.