High ammonia levels signify ...

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High ammonia levels signify anoxic/anaerobic conditions. 
If you want to eliminate the source, check of the river contains nitrificating organisms and look at ways to aerate the river water. 
Lowest cost would be the planting of aquatic plants known to oxygenate the water, though this would take some time to take effect.

Alternatively you can have a aerated biological stage (activated sludge or MBR) prior to your UF. Fast, but higher operating costs over time.

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