Almost half a million litres of wastewater has spewed into a river near Martinborough, after an "ongoing issue" at a treatment plant resulted in two discharges in as many weeks.

The incidents come after a year of water contamination problems for the South Wairarapa town.

E. Coli bacteria readings prompted boil water notices and sparked an independent review which said "it was a matter of luck" one of the incidents was not a repeat of the Havelock North event.

By the end of 2019 South Wairarapa District Council handed over water management responsibilities to Wellington Water, which is now dealing with the current wastewater overflow.

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What has been described as an "ongoing issue" at the Martinborough Wastewater Treatment Plant has resulted in a second discharge into Ruamahanga River this year.

Both events involved problems with the irrigator, which meant water was not discharged to adjacent land, and with storage ponds full, it ended up in the river.

Wellington Water said this was unacceptable.

The most recent incident happened on Monday between 9.20am and 11.30am resulting in the discharge of 100,000 litres of partially treated wastewater, as well as 300,000 litres of fully treated wastewater.

The other discharge happened between January 14 and 15, which resulted in 90,000 litres of partially treated wastewater flowing into the river.

Although discharging treated wastewater to the river is a consented activity under the right conditions, when the river is low, these types of discharges are invariably a breach of resource consent, Wellington Water said.

"Due to the dilution factor in the river, it's understood that public health and recreational water user risk from all discharges was negligible.

"However, Wellington Water is committed to doing better with how wastewater discharges enter the environment and are working on options for this. A full incident response and investigation of the outcomes of this work will be released when completed."

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Wellington Water has apologised for the delay in reporting the recent discharge to the council.

Authorities at Regional Public Health and Greater Wellington Regional Council as well as iwi and community liaison group representatives have now been notified.

As well as wastewater, Ruamahanga River is also is the grasps of deadly toxic algae, which is "quickly intensifying" throughout the Wellington region.

Greater Wellington Regional council's Otaki, Waikanae, Hutt, Ruamahanga and Waingawa river monitoring sites have exceeded the 20 per cent alert threshold, and the Waipoua River is above the 50 per cent "no swimming" line.

Today the council reported two dogs had died after ingesting the algae at Waipoua River in Masterton.