We had horrible problems with mud in the coops in the springtime (think boots sloshing down inches deep in clay/poo mud mixture). So... we had $80 worth of sand shipped to our house and we put it all in the coop. This solved the problem for about a year, until the sand ran off and began sinking into the clay again. So... we added more sand, and created a trench at the back of the coop where all the water gathers and runs off and away.
Thinking back, were I able to do things differently, I would have purchased a layer of rock first (to keep the sand from sinking), then put sand on top of it. This creates a perfect medium for chickens to be on. They love dirtbathing in it (especially after I sprinkle it with DE in the dry summer to keep the flies down), and it is basically self-cleaning when outside in the elements. Rain comes down, breaks and washes poop down, it flows to the drainage area and washes away. TADA! I love our sand run.
It is some investment in time and money to put it in, but it really is worth it. Better, healthier conditions for the birds and less work for me. It was worth EVERY penny.