I have the same problem!!! My coop I made so that my babies could go UNDER the coop from the hot sun...so what do they do when it rains....THEY GO UNDER THE COOP......AND I FLOOD!!!! I do have sand in my run...Ive put up roost all over which they use on very nice days....but when rain comes they dont like to get wet so under the coop they go.
Which means when it floods, and I mean about a ruler stick high, which would be about 12"....Im laying in my rain gear trying to stay dry, only to have to lay down and go swimming after my babies so they dont drown!!!! and its deep under my coop area, 2-3" deep....you should have seen us one day...soaking wet and swimming laying on the ground trying to catch them as they fought and floated, etc...
so now, when It rains heavy, I go and I try to block the bottom of the coop, of course DH works alot and we havent made anything to use, so I put boards, and chicken wire, IN DOWN POUR MY BABIES WILL STAND UP AGAINST THE COOP AND
NOT GO INTO THE COOP AWAY FROM THE RAIN!!!!!! Why do they do this?? They wont even use the roost...
ANY IDEAS ANYONE?? heres my coop and what it looks like where they go under:
the little side mini coop is gone...wish you could see a better picture of my main coop