Hi Layla,
I so do not like muddy runs, eww! One mistake that I have done over and over again, is trying to fix a muddy run when the grounds are still wet, in the end, its wasted time and wasted money.
Right now, your main concern is getting the chickens up and out of the mud. For a temporary fix to help get you through to the drier seasons, I would suggest using materials that are cheap, like organic materials as it will absorb moisture and will provide for the surface area to evaporate the moisture into the air. Whatever you can get your hands on, add lots of it into your run, the more you can put into the coop, the more effective it will be and the longer it will be effective. Keep in mind, the coarser stuff will decompose slower and last longer than your finer materials like straw and hay, but anything is better than nothing at all til you can make more perm. changes. If you only put a little inside, it will merge with the mud and make it worse. Mud is the enemy. A muddy run looks awful, gives us brown bedraggled chickens, stinks to high heaven, and breeds a lot more flies than a dry run does which I am sure you already know, thats why you are posting this. Mud is not good for the chickens. It can promote bumblefoot and internal parasites, as well as making it less easy and less pleasant for chickens to get around in it. The pleasures of winter huh?
If the coop is too flooded, a quick fix would be to use pallets, several high to keep the chickens out of the mud mess. I ended up tearing down my existing coop/run and building it on the highest ground of our property to prevent the water going into the run. You didnt state how big your run is, but this may reduce some of your flooding problem. I put gutters and downspouts on all the roofing, making sure that the downspouts were leading the water down and away. Non-perforated corrugated black drainage-tile pipes are cheap, they are long and flexible and make great extensions for downspouts. I also blocked where any rain might come through the top/upwind side of the run, a tarp works ok, but I prefer shadecloth over the two, it keeps most of the rain out. I am using corrugated roofing on my run now and the roof is slightly sloped so the wind and rain can push the water off the back side, away from the run. I also laid pavers around the run, slightly sloped, again to help the rain water wash away from the run. I use the deep litter method, and knock on wood, I havent had the run flood out once this year; looking good so far, but there are still a couple more months to go.
I so do not like muddy runs, eww! One mistake that I have done over and over again, is trying to fix a muddy run when the grounds are still wet, in the end, its wasted time and wasted money.


