I was a licensed Civil/Sanitary engineer for 35 years. What you all are describing does sound like some sewage overflow into the lagoon that is exceeding the natural assimilative capacity. If there is a lot of water infiltration into the sewers during rains, this is probably unavoidable without spending very large sums of money.
A simpler approach is to equip the affected area with some aeration tubes or floating mechanical aerators to supplant the natural treatment ability of the impacted area. This could be done pretty cheap although it would cost something to run as electricity will be required to supply compressed air or run the motors of floating aerators.
Another possibility would be to direct the overflows first into a naturally aerated lagoon dug out upstream for this purpose. The discharge from that could then flow into the regular lagoon and would have much of its oxygen demand satisfied before doing so.
Lagoons are a proven, low tech, low energy means of treating small to medium sized sewage flows. Properly constructed they will filter out the solids and kill the pathogens.
Aeration accelerates the treatment process and reduces the surface area of lagoons required. However, if there is plenty of space to construct lagoons, this is the better solution for the reason noted above, namely low/no energy requirement.
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