I would put #57 washed stone over top when you get it dried out. Then you can put wood chips or some other choice of bedding. welcome to BYC! and good luck with your drainage.
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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.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.