At least 57 flood-hit households in Christchurch are having to find somewhere else to live because their properties are potentially contaminated with raw sewerage.
Health authorities said the floodwaters have soaked the properties' carpets or made the foundations damp, making them unsafe to live in.
Kieran McGuire and his partner are now staying with a friend and do not know how long it will be before it will be safe for them to return, after floodwaters breached their floorboards and soaked through the carpet at their Beckenham rental property.
He was glad they managed to save their belongings before the water made its way in.
"We got everything up off the floor and couches and beds and stuff, we were able to prop up on books just to get it up off the carpet. It's amazing what you think of when you're panicking."
The clean up was not just happening inside. Council workers were out in force on Tuesday water blasting and shovelling the mountains of contaminated silt that was sticking to footpaths and roads like glue.
One home had all of its windows open, taking advantage of the sun to dry out the carpet and furniture inside.
The woman inside had come down from Napier to help her daughter and asked not to be named.
While the water did not make it inside, it came close to the floor boards, she said.
"All I know is that it's damp. You can just feel the cold and the condensation, it's pretty horrible. So the sunshine is great."
She was aware of the contamination risk and had already had expert cleaners around to sterilise the garage that did get water through it and ruined two cars.
She had also been helping to clear the toxic sludge left around the yard by the receding floodwaters.
"You just don't want that contamination going backwards and forwards. And then the 2-year-old, we're just lifting him into the car and out of the car, so he's only inside when he's here. We've kind of got three sets of shoes, [one for] the bad stuff, the middle and the clean."
The damp conditions underneath houses like this posed their own set of health problems, said Canterbury medical officer of health Dr Alistair Humphrey.
"Even if the flood waters didn't come above your floorboards, as they have done in at least 30 homes anyway, but even if they didn't, dampness can track up inside the walls of the house and it can lead to mould. And mould will actually get worse once the floodwaters have receded."
Dr Humphrey was urging people to leave the clean up to professionals, rather than trying to do it themselves.
"You should be wearing proper respirators to protect you from any mould that may happen and gloves and overalls to protect yourself from bacteria from the sewage and viruses. So it is a job, that if you are insured, my advice would be talk to your insurers first rather than try doing it yourself, it's far safer to get a professional to deal with it."
State of emergency lifted in Christchurch and Banks Peninsula
Christchurch mayor Lianne Dalziel said the immediate dangers posed by the significant rainfall and abnormally high tides had now passed and the state of emergency was able to be lifted.
Ms Dalziel said although the city was transitioning into a recovery period, the council was still monitoring river levels, tides, and weather forecasts very closely to ensure it is ready to react if needed.
While the city had a chance to dry out on Tuesday, further rain was forecast for Thursday, which authorities said may lead to further flooding in already affected areas.
Ms Dalziel said the forecast of further rain meant the situation was very changeable.
She said the council was working hard to minimise any impacts from the forecast rain by clearing flood debris from rivers, sumps and stormwater grates.
The council will also keep pumps deployed in Southshore and Flockton basin.