A method for treating livestock wastewater includes directing screened wastewater to a hydrocyclone/separation tank system. The hydrocyclone directs the wastewater stream in a generally helical fashion to create bubble-particle aggregates. Activating chemicals can be added to the wastewater upstream of the hydrocyclone or within the hydrocyclone itself. The wastewater is channeled from an outlet of the hydrocyclone through a diffuser to a separation tank, where the bubble-particle aggregates are separated as they rise and accumulate on a free liquid surface of the tank. The treated wastewater settles below the bubble-particle aggregate accumulation and is transferred to a reservoir for later use as irrigation water or barn wash water. Salts may also be removed from the wastewater by filtering the wastewater through salt-removing filters before the wastewater is transferred to the reservoir.