Green smelly algae

The outer run is under some trees. The area catches some sun. It has been so humid I’m hoping the humidity will break to dry it out. I’m not sure if it will die off it looks so green.
Since the run looks permanent, you could trench around the outside and add rock. Time consuming but we had algae issues in our last home’s back yard that backed to a dry creek bed. The ground was just too wet from the sump pump and rain run-off so we got some dirt, elevated the low spots above the dry creek only a few inches, added two trenched drains to the lowest corner of the lot and put in a small pit full of gravel. It worked quickly. No more algae or stench.
I would remove the cover and let the sun dry it out. Some green algae is toxic so you might want to remove the areas that have it and add new soil. Hydrogen peroxide sprayed on the algae might also help in the meantime. Of course, when chickens are inside. And, everyone says mulch for muddy ground.
We leveled the untouched-for-decades ground under our greenhouse last summer but over the winter, areas still dropped. It happens.
Hope this helps!
 

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