I need to keep water out of the run

OP needs to solve the drainage problem first, then can tackle the issue in the run by building a good deep litter. Until the drainage is taken care of, any DL put in there is going to turn into an anaerobic stinky mess.

I would trench around the entire run, remove the soil from the trench, replace it with pea stone, and put the removed soil into the run to build it up at least 2 - 4" above the outside area. Then, start building a deep litter in the run.

The other option is to look around the yard and see if there is a high spot. Move coop and run to the better location.

Often folks use the worst section of their land for their chickens/garden. You must have good drainage for either to prosper.
 
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The pine shavings have been working great in my coop. The concrete walls leak water when it rains as the dirt ramp to the hayloft is along the wall and it has a large volume of water from the barnroof soaking into the ground right there. The wood shavings soak up the water nicely and dry out fairly quick if given a chance. They will break down fairly quick outside, so OP will need to keep adding shavings. I think they may be a bit easier to work with in the small area that she has - both for spreading and for cleaning out.

I take the bag into the coop, dump a pile of new shavings in the center of the coop and sprinkle on some sunflower seeds. It is evenly spread across the entire coop within an hour...
 
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Does the ditch slope down away from the coop? The ground looks sorta flat, for a ditch to work it must have a small downward slope toward the direction of intended flow.

Edit: looking at your original photos the base of the run is containing the water like a dam. Unless it has some way to go under the bottom of the run it will just stay in the run. Dig a hole under the boards and put some gravel in so the water can pass through. The side shot of the coop and run looks like you have quite a bit of slope, you just need to let the water out.

JT

Does the ditch slope down away from the coop? The ground looks sorta flat, for a ditch to work it must have a small downward slope toward the direction of intended flow.

Edit: looking at your original photos the base of the run is containing the water like a dam. Unless it has some way to go under the bottom of the run it will just stay in the run. Dig a hole under the boards and put some gravel in so the water can pass through. The side shot of the coop and run looks like you have quite a bit of slope, you just need to let the water out.

JT
The only reason I didn’t do tha is because about 2-3 feet in front of that slope the ground rises up a bit and I didn’t want to dig that up as well then next thing you know I will have a portion of the yard dug up. The yard does slope some because I had to have an area between the coop and the house graded because water literally pooled in it all winter long and it started eroding the foundation. It is so frustrating because it almost seems like the coop is sitting in an indentation. We are supposed to have rain starting this evening continuing through tomorrow afternoon with 2 inches and possibly 3 inches in some areas then rain again this weekend. The area around the front of the coop is already squishy from the rain we had day before yesterday. Such an aggravation. Dad gum clay soil. The girls will get sick from standing in that water. For so long. I have 5 60 lb bags of sand that I could put in there but with it raining......I am 72 years old and while I feel like I can do all of this heavy work I just don’t have it anymore. I spread 5 of those bags about a month ago and I had to pull them out of the trunk and slide them in a little wagon that I put flush up against the car and just have to huff and puff to turn the wagon over so the sand can fall out. It is just pitiful I had to go and get old (or be grateful depending on whether my glass is half empty or half full that day) I have thought about getting thick pavers and use them as a floor. I just can’t think of what to do and here comes all. that rain.
 
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Tree services have to pay junk yards to let them drop off a load of wood chips., and they have to travel to get there. They would love to be able to drop them somewhere close to where they are working and not have to pay. They will gladly drop the chips on your property for free! It's cheaper for them and they don't have to travel to the dump. Just call some local tree services and ask.
I called 2 tree services and one just said no, they didn’t do that and the other wanted $35. Charity must be absent in this part of the world:hmm
 
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Does the ditch slope down away from the coop? The ground looks sorta flat, for a ditch to work it must have a small downward slope toward the direction of intended flow.

Edit: looking at your original photos the base of the run is containing the water like a dam. Unless it has some way to go under the bottom of the run it will just stay in the run. Dig a hole under the boards and put some gravel in so the water can pass through. The side shot of the coop and run looks like you have quite a bit of slope, you just need to let the water out.

JT
The only reason I didn’t do tha is because about 2-3 feet in front of that slope the ground rises up a bit and I didn’t want to dig that up as well then next thing you know I will have a portion of the yard dug up. The yard does slope some because I had to have an area between the coop and the house graded because water literally pooled in it all winter long and it started eroding the foundation. It is so frustrating because it almost seems like the coop is sitting in an indentation. We are supposed to have rain starting this evening continuing through tomorrow afternoon with 2 inches and possibly 3 inches in some areas then rain again this weekend. The area around the front of the coop is already squishy from the rain we had day before yesterday. Such an aggravation. Dad gum clay soil. The girls will get sick from standing in that water. For so long. I have 5 60 lb bags of sand that I could put in there but with it raining......I am 72 years old and while I feel like I can do all of this heavy work I just don’t have it anymore. I spread 5 of those bags about a month ago and I had to pull them out of the trunk and slide them in a little wagon that I put flush up against the car and just have to huff and puff to turn the wagon over so the sand can fall out. It is just pitiful I had to go and get old (or be grateful depending on whether my glass is half empty or half full that day) I have thought about getting thick pavers and use them as a floor. I just can’t think of what to do and here comes all. that rain.
 
I called 2 tree services and one just said no, they didn’t do that and the other wanted $35. Charity must be absent in this part of the world:hmm
Cheap buggers! Try contacting your local municipality to find out when they trim trees along the roads and ask them. MEANWHILE get some pine shavings, not very pricy at all, the bales are not as heavy as sand!! And they are compressed so much that they hold tons more than it looks like îs in there.
 
MEANWHILE get some pine shavings, not very pricy at all, the bales are not as heavy as sand!! And they are compressed so much that they hold tons more than it looks like îs in there.
This may be your best, or only option, at this point.
Really you need fill dirt to raise the whole area that the coop and run sits on.
 
A caution here... make sure if you fill in with dirt it must raise the entire run AND coop. Otherwise the coop will be lying in a dirt bowl and turn into a pond surrounded by the dirt run.

Why does the coop have to be raised? It's not in a dirt bowl now, is it? Raising the run would be best, but if she can't do that raising the level of the ground there would keep water from draining into it.
 

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