Drain flies(?)

Photos of your run, please?

Coarse wood chips, the sort that you get from a tree-trimming service, are often considered the gold standard for the control of mud, but if the root of your problem is bad drainage there is nothing to do except improve the drainage.

If you show us photos of your run and it's surroundings we can probably help you get the water under control and that will eliminate the pests.
 
My muddy run has what I think are drain flies. How would I get rid of them without pouring more liquids in? Would they cause any problems?
You need to dry out the run, not add any liquids.
Correcting any drainage problems, stopping any water running into the run from nearby roofs, slopes,and hardscaping is the first course of action.
Adding absorbent bedding is the next step, coarse wood chipping from a tree trimmer are the best, IMO.
Post pics of your run and the surrounding area and you should get some suggestions on how to help it.
 
If it is drain flies, they will not cause any problems. But muddy runs are not only unpleasant to work in but they can cause other problems. After a while they can stink, they might harbor diseases, and if the chickens can't get out of the mud they can develop foot problems. When the weather sets in wet it can be really hard to keep your run dry but as long as it dries out when the rain stops it's not usually a big problem.

To me there are two basic ways to approach it. The larger the run the harder this can be. First is to keep the water out. Where is the water coming from? Rain doesn't just fall straight down, it can blow in from the side. Is ground water running into the coop, Aart covered a lot of possibilities for that. If your run is in a low area where water drains to it an collects you may have a real problem.

The second approach is to get the water out once it gets in. If your soil were sand which drains well you probably would not be writing about it. You probably have clay which holds water. If you have a place where the water could drain to you might be able to help yourself by using some type of French drain. It doesn't have to be pipe, a trench filled with sand or gravel can work. Another approach is to build the area up so it does drain, maybe putting in a layer of gravel then topping it with sand. But the water still needs a place to drain to, if you dig a hole (or it is in a low spot to begin with) and fill that hole with gravel or sand, all you've done is create a bathtub to hold water. It does depend on what the area around it looks like.

Some people get success with adding some type of mulch like Aart's wood chips. Depending in conditions it may be a permanent solution, it may be temporary. If they stay wet organic materials like hay, straw, wood shavings, dried leaves, and such can break down and become a problem themselves and need to be removed. Wood chips take longer to break down so they are often a pretty good choice. People use all of them with varying degrees of success. Some people turn their runs into a compost pile, which can help, but it needs to drain for this to work well.

A lot of what you can do depends on the lay of the land and the type of soil you have. Like may things with chickens, what works for one may not work for another because our situations are different. My run is on a small rise so it drains fairly well but it is a silty clay. When it gets wet it can be a mess to work in but the chickens have a drier place to go so I don't worry about those foot problems. I poured some pea gravel in strategic places so I can walk in there without getting real muddy and used pavers to create a dry path to the back of the run. Some people use pallets or some form of wood to get them and the chickens up out of the mud. I can live with mine since it drains before it stinks or causes health problems.

Good luck!
 
So, not quite a run, but in my dirt-floor coop (conversion from a 3-side shed to a full coop), my solution was to just raise the ground. Water seeks the lowest area and if your run is higher than the surrounding area, the water will head to the surrounding area and the run will quickly dry off after the rain stops. Additional mitigation can be done by covering part/all of it. Then beyond that, just keep adding woodchips into the run. The chickens will move them around as needed, they will help absorb moisture/stink and eventually break down into more dirt, which can be shaped to have the high points inside the run.
 

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