Help! Winter run maintenance- PU!

Roofing the entire thing will help, however if you have drainage issues where water from outside the run flows into the run area, you will still have problems with mud or pooling water.

I also use deep litter like many folks above, mainly aged chunky wood chips as a base with dried leaves, dried grass, garden clippings, as I get them. I used to have a massive mud issue and my boots were sinking into it and sticking, and now that's completely fixed and the run stays drier than the rest of the lawn, even though it's unroofed and we get heavy rains. However I have no existing drainage issues in the run, so simply adding the litter naturally fixed it over the course of a few months, as the litter allowed water to drain through into the porous soil beneath, while creating a dry surface on top.
 
Roofing will be a big help, but as @rosemarythyme and @aart pointed out, drainage issues need to be fixed first, if you have them.

Aging wood chips first, or at the very least, letting them dry in the sun, prevents the growth of mold in your run. Some of these molds re deadly, and could wipe out your entire flock. It doesn’t happen all that often, but you wouldn’t know until the chickens got sick.

Leaves raked up from the yard, grass clippings, garden scraps and cleanup, pine cones, and twigs can all become part of your litter.

I was astonished to discover that my deep-litter run doesn’t smell! It doesn’t get very wet except in summer, when part of it is unroofed. I’m sure the hens will be happier when they have more sunshine in the spring, but it would fill to the top with snow if there were no roof.
 
I was astonished to discover that my deep-litter run doesn’t smell!

That's the best way to check that the litter is working properly. Once it's established, even after days of rain you should be able to crouch down in the run and not really smell anything, other than maybe some fresh cecal poop.
 
We had a lot of problems with mud in our run the first six months that we had it as an open air run. It was difficult to figure out how to keep the run dry, but keeping it dry-ish has turned out to make a huge difference. We have heavy clay soil that doesn’t let water drain through, and the chickens had dug out the middle, so we had essentially a bathtub or pond that held muddy water. Over a few months, we did the following: Covered the run with tarps or shade cloth, and that helped but we still had a lot of water seeping in from the sides. We next built a trench to divert water from the run, and added a rain gutter to the uphill run side to catch the rain from the tarp. Last, we added coarse wood chips that were a byproduct of clearing cedar trees last year. I’d like to have the 12” deep litter, but that doesn’t work too well with the rest of our setup so it’s only 3-4 inches deep. We layer in new material, like leaves, straw, more wood chips, etc as needed. We also toss scratch so the chickens turn the run material over. We have 28 chickens/ducks in a 450 sq foot run and this current system is still not perfect, but much much better than the disgusting mud that we had last winter. Good luck with your setup! I’m sure you’ll find what works for your situation...
 
Wood chips are great. Be careful .Black walnut chips are toxic to many animals .Tree surgeons don't care what they chip into the truck
.I know of at least two times ,walnut chips used as stall bedding has killed horses.Red woods like ceders are slow to break down in compost if at all.
Dense hardwoods take longer too .They also make soil more acidic. You want to either check the ph of compost and soils conditioned with wood chip compost .Use hydrated lime to adjust the Ph.I would remove the chickens brodcast a heavy gound cover of lime cover with wood chips . Microbs are our friends make a home for them .
 
You can use any sort of dry to make layers. I use hay or straw, shavings, chips, leaves. If you use a tarp, make sure all the eyes are locked down, else wind will snap it like anything and pull the eyes out where you do have them tied. Also maybe put a pole up tied to 3 or 4 sides so that water doesn't pool.
I've been battling with tarps for yrs. I hate the dang things lol. No more though, new coop is ready, moving day is Thursday. New fence coming Sat.
 

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