The effluent bloom created a horrid stench in the Wellington coastal suburb of Houghton Bay.

Wellington's old pipes were once more overwhelmed by heavy rain creating a stinking bloom of effluent one passerby described as a "code brown" horror.

Island Bay's Michael Lanzensberger was driving home through nearby Houghton Bay on the South Coast when he was confronted by a disgusting smell on Thursday night about 6pm.

"It was a code brown. It smelled like a sewer. It smelled like it looked. It was quite horrid," Lanzensberger said.

KEVIN STENT/STUFF Dr John Robinson holds a section of the smelly brown sediment that streamed from an outflow pipe in Houghton Bay in 2013. (File photo)

MetService figures show 21mm of rain fell between 5.30pm and 8.30pm on Thursday, including an hour-long heavy burst that dumped 8mm.

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The heavy rain created a bloom in the bay - a popular surfing spot - but residents have been plagued for decades by the problem of stinking effluent.

MICHAEL LANZENSBERGER The leaching is caused during heavy rain from run off from the old Houghton Valley landfill.

Wellington Water community engagement manager Alexander van Paassen said the problem was probably caused by silt and dirt runoff from nearby subdivision work collecting at beachside sumps.

"Below the new subdivision which is under construction adjacent to the beach outlet, the roadside sumps were full of silt and dirt which had obviously runoff from the sites under the heavy rainfall [Thursday] night.

"There is often a decaying organic-type odour present at the outlet. This is typically due to the seaweed build-up in the area."

A maintenance programme was in place to minimise overflows but van Paassen said studies had shown that while unsightly, the impact on the affected environment was relatively minor - in part because the effluent was highly diluted.

Staff, who were on a fortnightly inspection roster, had been to the site and checked the weir and diversion.

The last programmed inspection was carried out on October 18, when the pipe was cleaned of leachate grit.

As well as regular inspections, the stormwater pipe is flushed about every six months to remove any leachate encrustation. There is also an alert that triggers if the weir is over-flowing in dry weather.