Testing of Whakaraupō/Lyttelton Harbour has found human and animal waste contamination is present after rainfall, Canterbury Regional Council says.
The council announced it would conduct further testing in January when a number of popular beaches in the harbour were graded unswimmable over summer due to the risk of contamination.
The council's surface water science manager Dr Elaine Moriarty said they used faecal source tracking to determine the origin of the pollution following rain.
Corsair Bay had human and bird waste present in all samples. Some also had dog and livestock pollution present too.
At Cass Bay, human contamination was found at the main beach and in two waterways.
One stream in Rapāki Bay showed bird and human pollution, while Diamond Harbour beach and stream tested positive for human, livestock and dog contamination.
Purau Stream had positive results for human, livestock and bird waste, with livestock and bird contaminants also detected at Purau Beach.
In Akaroa Harbour, Akaroa Beach and Glen Bay both had human, bird and livestock pollution present.
Canterbury medical officer of health Dr Cheryl Brunton said contact with contaminated water could cause sickness.
"Water contaminated by human or animal faecal matter may contain a range of disease-causing micro-organisms, such as viruses, bacteria and protozoa, which can cause gastrointestinal, respiratory, and skin infections."
People should always check the water quality before swimming or collecting kai, Brunton said.
"As a precaution, avoid swimming in the harbour, rivers, streams, lakes or estuaries for at least 48 hours after heavy or prolonged rainfall, even at sites that usually have good water quality.
"People should also avoid eating shellfish and mussels from the harbour after heavy rainfall. If fish are eaten, remove the gut and liver and wash them in clean water before cooking."
Moriarty said the council was increasing monitoring by doing extra testing over winter.
"This is part of our project to move towards a live modelling monitoring system which would allow us to make continuous predictions of water quality for recreation," she said.
"In many bays water quality fluctuates, especially after rainfall. When live modelling is launched, swimmers will be able to find out if a bay is safe for swimming on any specific day. This is still some time away, but we hope to have it live in future summers."
Christchurch City Council was now leading an investigation into how the contaminants were entering waterways.
"We are working with Christchurch City Council, Te Whatu Ora, and local iwi to share information and assist with further testing where required. Public health is a top priority for all three agencies as we work together to improve water quality in Banks Peninsula," Moriarty said.
The city council's acting head of Three Waters Brent Smith said finding where contamination was coming from was a big job because there were so many potential sources.
"The sorts of things we'll be looking into include leaking septic tanks on private property, damaged public and private pipes, wastewater overflows, private cross connections, boats dumping wastewater, and freedom camping," he said.
"One of the first steps we're taking is to carry out further sampling in two areas during periods of dry weather. This will fill in some of the gaps and supplement the sampling done over the summer period and following rainfall events."
The investigation was expected to take some time.
But Smith said: "Everyone plays a part in helping keep our waterways clean and healthy," and there were some immediate actions that would help reduce contamination levels".
People were urged to report any spillages, leaks, or pollution seen near waterways or drains, pick up dog poo and use public toilets.
Boats should be compliant and any sewage waste disposed correctly.
Septic tanks should also be checked.