Depending on where you live, if it is in a more modern area subdivision type community, most homes once built, the yards are filled in with fill dirt before sod is laid down for the grass. Fill dirt can contain all different kinds of materials in it, not all of it good.
If you are living in a rural setting, then you can have soil analysis done by your county extension agent for little to no cost. You can also have that done by them if you live in the city. Pat from Canada gave some excellent advice regarding trenching around the runs, putting gutters around the coops and downspouts with lines running away from them. You can actually set up a catch barrel to use the rainwater in the garden on the downspouts as well. Or if you live in the country, and have a lower part of the property you can build a holding pond to contain the runoff.
I should have been clearer in my advice about tilling the soil in the run. You actually want to get down to the subsoil when you till. If you are, as Pat stated on hardrock or clay, then you need to put a layer of gravel down first, then put some landscaping cloth over that, then start by putting a layer of wood chips, peat and dirt mixed together down first. Mix this well then you can build up the soil in the run before putting the sand down.
You can also use gutters to trench around the runs, just put hardware clothe over them to keep debris out of them.
Hopefully once I get started on the coop and run I will be able to take pictures and post them of the work in progress.