Good for you thinking about this problem BEFORE you build the coop.
My first suggestion is going to be uncomfortable, but it's worthwhile.
Get a good big handful of landscape flags, maybe in different colors, and then the next time it's raining REALLY HARD, put on your rain gear, go out in it, and mark the places where water runs through the landscape, where it pools, and where, hopefully, you have a high-and-dry spot.
If at all possible, build on that high and dry spot.
Additional measures you can take include:
- Installing French drain -- either the traditional gravel-filled ditch @Ted Brown mentioned or the modern plastic pipe sort,
- Digging diversion ditches to lead water around the coop,
- Creating grass swales to lead water around the coop,
- Building up the land to create that high-and-dry island in the topography.
- Have your land professionally graded to manage the water runoff. This can be a surprisingly affordable option -- as we discovered when the installation of our septic system left piles of spoil that screwed up our drainage. A knowledgable "man with a bobcat" improved the entire property's water flow with just a couple hour's work. Probably not worth it for just a chicken coop, but if you've got other water issues on the property it's a good investment.
I personally would only use the gravel and landscape cloth technique that
@SourRoses mentioned under a building where the chickens would have no access. Chickens are champion diggers, landscape fabric deteriorates, and chicken poop + gravel + water = stench.
In the run, a deep layer of coarse wood chips is probably your best solution, in combination with the water management options listed above.
Here's an excellent article:
https://www.backyardchickens.com/articles/how-to-fix-a-muddy-run-chicken-coop.47807/