Ok jdragovits, if the filter is the rocks in the return, you don't have enough biological filtration.
1) UV sterilizer would be the quickest solution. (make removable for winter storage so freezes won't damage it).
2) Barley straw takes 3-6 months to work and is marginal.
3) Plants. Bog plants (local cattails, papyrus, etc) in the 'filter' rocks & set on blocks to hold them up in the pond.
Since your season is waning, I would clean the pond well and get it ready for winter and implement these in the early spring in the above order.
How long has the pond been up?
You didn't state what fish (bio-load) you have in there?
Does it freeze over in the winter?
Dr Joe
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