It sounds like you have metals in the water, which isn't a surprise for river/stream water. If that's the case, high chlorine will cause the metals to precipitate out and create the brown color that you're reporting. Can you take a water sample to the pool store and ask them to test it for metals?
If you do indeed have metals in the water, then you'll either need to add a metal sequestrant to keep them in suspension (these are broken down by chlorine, so when you see the water starting to discolor again you'll need to add another dose) or to filter the metals out of the water by running it by a high chlorine source right before it goes into a filter, so the metals will drop out on the filter and you can get rid of them that way.
What type/size of pump and filter do you have on this pool? What are you using to test your water with, and what are your levels for pH, alk, and CYA?
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