The Clean Water Branch was notified of a second discharge of 1,500 gallons that flowed into Kalihi Stream early Saturday evening.
The discharge occurred at about 4 p.m. and stopped an hour later.
The public was advised earlier to stay out of the stream due to an initial overflow of nearly 7,450 gallons of untreated wastewater.
City Environmental Services responded to a residence on Alu Street around noon Saturday after a sanitary sewer overflow. Officials say roots clogged a 12-inch pipe causing the water to flow into the stream.
The State Department of Health says the discharge was stopped around 1:45 p.m. and warning signs have been posted downstream to the mouth of Keehi Lagoon.
Crews are in the process of cleaning, disinfecting and de-odorizing the affected area near the overflow.