It is the third time in a month that contamination levels in the bay have exceeded safe standards.
Wellington City Council is urging people to stay clear of the water in the area until further notice.
The Council's Infrastructure Planning Manager, Maria Archer, says water-quality monitoring this week has again found that the presence of enterococci - an indicator of microbiological pollution, including sewage - in Owhiro Bay is at a level likely to cause a health hazard.
The Council has taken the action following consultation with Regional Public Health staff.
Ms Archer says the repeated beach closures are "obviously frustrating".
"The intermittent nature of the spikes in contamination levels also makes it harder to track the source down."
Ms Archer says Council staff have located and fixed sewage leaks in Severn Street and in the Todman Street area in Brooklyn, at the top of the Owhiro Bay catchment.
They are now also inspecting the sewer main in Owhiro Parade and continue to do tests and inspections up the Owhiro Stream. She says, however, that staff are confident the source is not at the Southern Landfill.
If fractures are found, repair work will be done as a matter of urgency.
Ms Archer says staff will concentrate their efforts on finding the source or sources. "We won't be happy until this problem goes away."
The presence of enterococci in the water indicates it is unsuitable for swimming or recreational contact. Health problems that can be associated with the ingestion of contaminated water include diarrhoea, stomach cramps and vomiting. In addition, cuts and skin lesions can become infected.