Transformation of ammonium to nitrate upon sewage discharge to sub-surface environment exposes about 65 million households in rural and urban India to risks of drinking nitrate contaminated groundwater. Building on earlier research, a twin pit is modified in Mulbagal town, Karnataka, to remove nitrate in pit toilet sewage and is functional for nearly one year. The first pit serves as an anaerobic chamber, while the second pit facilitates aerobic reactions in the upper half and is equipped with a bio-barrier in its lower half. Quality of treated sewage is monitored by soil water samplers installed adjacent to the pit. After anaerobic digestion in pit 1, sewage flows into the aerobic chamber (upper half of pit 2), where COD/N ratio of 1.49 to 1.73 facilitates aerobic conversion of ammonium to nitrite and nitrate ions. Annamox reactions in a bio-barrier chamber (lower half of pit 2) reduce ammonium and nitrite concentrations, while denitrification reactions in the bio-barrier remove nitrite and nitrate from pit toilet sewage. Besides nitrate, the modified twin pit reduces COD (chemical oxygen demand), ammonium, and thermotolerant coliform levels in the discharged sewage.