Students use the Beaver Rd bridge to cross the Taylor River going to and from school.

Just when you thought it was safe to go back in the water, a poo report might make you think twice.

Ten coastal beaches and seven river sites in Marlborough were sampled weekly over summer for faecal contamination indicators, and for some spots the results are pretty stink.

The worst-of-the-worst, unsurprisingly for some, was the Taylor River, in Blenheim, with about 60 per cent of samples having an 'unsafe' bacteria concentration of more than 550 E coli per 100 millilitres.

SCOTT HAMMOND/STUFF The Taylor River flooded on Tuesday following prolonged rain.

Marlborough District Council environmental scientist Steffi Henkel, who presented the report to the council last week, said genetic sourcing proved human fluids were one of the contaminants in the river.

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Blenheim resident Marg Foxton was walking along the Taylor River on Tuesday and said the results were "absolutely shocking".

SCOTT HAMMOND/STUFF Children playing in the Taylor River in January.

"I can understand there being animal poo, but I can't believe there's human," Foxton said.

"I heard about this sort of thing when I travelled to India, but I never thought we'd have it here."

Samples were tested for faecal contamination indicators, which were Enterococci in coastal samples and E coli in river samples.

RICKY WILSON/STUFF Warning signs explain the risks to people using the Taylor River reserve.

Both bacteria had the potential to affect the health of recreational water users.

Scarlett Sheridan, who grew up just outside Blenheim, said she wasn't surprised there was faecal bacteria in the Taylor River.

"My parents never let us swim in the river as kids," Sheridan said. "I never wanted to swim. Never saw the appeal.

SCOTT HAMMOND/STUFF Scarlett Sheridan, who grew up just outside Blenheim, says she "wouldn't be surprised" if there was faecal bacteria in Taylor River.

"This is just more of a reason not to go swimming in it."

About 25 per cent of Taylor River's samples taken from the beginning of November 2017 until the end of last month returned with 'safe' levels of faecal bacteria, which was under 260 E coli per 100ml.

Henkel said permanent warning signs were erected over summer as earthquake damage to sewerage and stormwater infrastructure caused contamination to stormwater.

SCOTT HAMMOND/STUFF Blenheim resident Marg Foxton says the results are "absolutely shocking".

"Repairs are ongoing," Henkel said. "We will continue monitoring [the water] once constructions are finished, just to ensure that the repairs will result in better water quality before we take the signs down."

Council freshwater ecologist Peter Hamill﻿ said while he was "unsure" when the water quality would return to 'safe' levels, it would "not happen over the winter period".

The second worst offender was Ngakuta Bay, located just outside Picton, which showed "unusually high bacteria concentrations" in the report.

CHLOE RANFORD/STUFF All samples taken from Mistletoe Bay had bacteria concentrations within 'safe' levels.

Samples taken from the bay's coastal waters showed about 15 per cent of results were 'unsafe' and about 15 per cent of results had an 'increased risk'.

Henkel said rainfall could be behind Ngakuta Bay's high levels of faecal bacteria.

She also said overflowing septic tanks might have contributed to the high levels.

SUPPLIED The report shows Ngakuta Bay is the second worst offender in Marlborough, with "unusually high bacteria concentrations".

The water quality at Picton Foreshore was listed as much cleaner, with about 90 per cent of the foreshore's samples resulting in a 'safe' grading - good news for midwinter swimmers on Sunday.

Henkel said she was "surprised" Picton Foreshore had lower levels of faecal contamination than Ngakuta Bay, considering Picton housed about 1400 more properties.

"We will have to, in future, investigate why this happens here," Henkel said. "This is not something that's going to go away."

She suggested the council consider checking Ngakuta Bay septic tanks with more frequency.

"A lot of other regions have protocols in place where the council checks septic tanks," Henkel said.

"Quite often people install septic tanks then forget about it, but these systems have to be maintained."

Other locations with a 'safe' reading of about 85 per cent or less included Okiwi Bay, Anakiwa, Momorangi Bay and Waihopai River at Craiglochart.

The report said a small number of samples at Momorangi and Robin Hood Bay had high bacteria levels during dry weather conditions, but these remained isolated incidences.

It also said a wet second half of the summer resulted in guideline breaches at most of the sites tested, as surface runoff caused by rainfall elevated bacteria concentrations.

But despite the wet summer, all samples taken from Mistletoe Bay and Waikawa Bay had faecal bacteria concentrations below guideline levels.

The report said this was "particularly encouraging" for Mistletoe Bay.

"Recreational water quality at this site has improved significantly since a contamination source was found and removed following an investigation into high Enterococci concentration during the previous season," the report said.

The annual report was received by the council and would be used to direct next year's sampling.