Been raining a lot

Mud itself will not make a chicken sick. It is the protozoa and parasite larvae, and germs in the mud that can cause trouble.

If your run isn’t covered that would be something to consider.

Adding sand (not “play” sand. River or all purpose sand which is larger grain)
Gravel, pine straw , grass clippings , leaves, straw ...anything really, which can get their feet up out of it, and promote faster drainage would help your situation.
 
I've been thinking about this too. Mud provides a better breeding ground for parasites/worms. And, since they can't dust bathe, they could get mite-y..?

If they have dry areas to hang out, and hopefully dust bathe, it can help. A pan of dry dirt is sufficient.

If they "catch a chill" they can get sick. They don't mind hanging out in the mud and rain... But need dry refuge. Keep an eye for excessive sneezing...
 
Just a couple more thoughts to those that have already been stated, if it's very wet, and stays that way then organic materials may cause mold growth, which would just make things worse. Short term things to absorb moisture can work but you have to watch for mold and change sodden stuff out often. Long term, fixing/improving drainage is far better. If your set up is near a roof from another building it can add a lot of water from run off, so if that was redirected away it might help if it's a contributor.
Another thing to be aware of is mud balls or poop balls on legs and feet and toes, which can happen in muddy conditions, can build up and dry very hard and can cause discomfort and problems. Here is a link, just watch for that until things dry out and do some foot cleaning if necessary.
https://blog.cacklehatchery.com/how-to-remove-dried-mud-caked-on-a-chickens-shanks-and-toes/
 
My run flooded it was over my ankles. I’ve been hauling dirt (my aching back) built a berm all around the coop and am trying to provide a natural flow for drainage. One of those things I just cannot put off any longer in winter I have the same problem from snow. I’m lucky I guess because my run is kinda small. I’m lucky too that in the desert we don’t have flee’s or ticks. I worry most about mosquitoes (standing water) they can carry lots of diseases. God bless BATS!!
 
I had to rig up a gutter off my main coop directing water away from the pen out into the yard, it works. Tarps draped down over the sides of pens help, and can be rolled up and secured until it rains again.
Sand is the best thing to put down in pens, layer it up at least 6 inches because hard rains will beat it down into the soil. Sand absorbs water, doesnt puddle, wont wash away, dries quicker and deters parasites. I have a 25'x25' pen and it takes about 4 cubic yards of sand to fill and spread. Here, it costs about $25 per cubic yard. Think beach. :)
 

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