Wastewater has been mistakenly flowing into Owhiro Stream for eight years. (File photo)

Wastewater has been mistakenly spilling into a Wellington stream for eight years after pipes were incorrectly laid in a new subdivision.

Wellington Water said on Wednesday it had found and fixed five cross-connections since January at a subdivision in Happy Valley.

The cross-connections meant wastewater pipes were mistakenly connected to stormwater pipes which flowed into Owhiro Bay.

Wellington Water said the mistake occurred when the subdivision was built about eight years ago, and there were likely to be more cross-connections that it had yet to identify.

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Spokesman Alex van Paassen said the pipe layout would have needed Wellington City Council consent.

MONIQUE FORD/STUFF The stream has recorded varying levels of contamination in recent years. (File photo)

"There would have been a sign-off process for plumbing connections."

The council-controlled organisation has been investigating water contamination problems at Owhiro Bay since January.

That work had led to the discovery of the cross-connections.

The error was one of the reasons for fluctuating water contamination readings in the bay in recent years.

On March 1, a sample from the Owhiro Stream outlet detected 23,000 colony forming units (CFUs) per 100 millilitres of water. The safe level is less than 240 CFUs per 100mls.

In the six days from February 28 to March 4, four readings showed contamination levels thousands of CFUs above safe swimming levels.

NIKKI MACDONALD/STUFF Residents have been complaining about contamination in the stream for years. (File photo)

The cross-connections were just one of the reasons for the inconsistent water readings, van Paassen said.

Water samples taken for testing were relatively small and not always reliable, and other contamination such as bird faeces could also enter the stream.

"But the cross-connections aren't helping."

On Wednesday, contractors flushed out the stormwater pipes to get rid of any residue stuck to the sides of the pipes from wastewater flows.

Residents would not be affected by the work, van Paassen said.

In January, it was discovered wastewater from a Cuba St apartment building had been spilling into Wellington Harbour for at least 10 years because of crossed pipes.

Wellington Water said at the time there were likely to be more cases of cross-connections across the city.

A Wellington City Council spokesman said at the time staff would need to delve deep into its archives to figure out when and how the mistake occurred.