The disclosed lagoon biological treatment system helps existing wastewater treatment facilities meet stricter discharge permits mandated by the EPA utilizing a facility's existing wastewater treatment infrastructure. Influent is pumped into and processed in an aerated or non-aerated lagoon system, thus initially treating the wastewater to remove BOD5 (Biochemical Oxygen Demand) and TSS (Total Suspended Solids) down to approximately 20-30 mg/L. Then the wastewater is transferred to and processed in a nitrification reactor that is designed to maintain a minimum water temperature needed to further treat the wastewater to stricter EPA standards. Wastewater may also be further processed in a denitrifying reactor if necessary to meet local requirement. Finally, effluent water is sent to a settling lagoon for final clarification prior to discharge.