Disgusting chicken run

Has anyone else dealt with this kind of thing before?
First, does the water gather/puddle there in the run, was there standing water there before chickens, or drain off to adjacent areas?
Gutters on nearby roofs and/or trenching and/or swales can keep some of the rain water out of the run.
How about a real roof on the run instead of tarps?

maybe because it's mixed in with a bit of straw and organic matter
You probably need more organic matter...a good mix of sizes, shapes, materials to 'eat' the poops and ameliorate the mud. Straw can be an ingredient, but bigger wood chips and other items are needed to balance the mix.

Here's a great description of contents and how to manage organic 'bedding' in a run or coop...and there's a great video of what it looks like.
http://www.backyardchickens.com/t/1037998/muddy-run-help-please#post_16017992
 
I'm also in Pac NW and my entire run is uncovered despite the rain. Like aart said, assuming there's no drainage issues in your run area using a variety of different sized bedding materials, like chunky wood chips, clumps of weeds, dried leaves, garden trimmings, will allow water to drain through and keep the run from turning into muck. As the material breaks down you can shovel some out for your garden (or offer it to a neighbor who does garden) and then add more material. You might be able to get wood chips for free from a tree trimming company, if you ask around. But using just wood shavings will get soggy and hold onto moisture.
 
What if you muck out the run in the problem area, dig a trench, and put in a french drain with a lot of gravel? Then cover the gravel with dirt/pine/mulch/lawn clippings/leaves etc?

It sounds like there is nowhere for the rain to go so it just sits. It might need help getting in the ground.
 

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