People in Tākaka, Golden Bay, are being asked to try avoid contact with floodwaters as some sewage pump stations overflow.
The Tasman District Council said stations in Tākaka were struggling to cope with the amount of water and there are overflows at some point.
"These overflows contain raw sewage and people must avoid contact with these areas. Please treat all surface water as potentially contaminated."
The fire service has also been pumping water from properties in Pohara.
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There are orange rain warnings in place for parts of Nelson and Tasman, with Golden Bay lashed with rain overnight.
Nelson-Tasman Emergency Management said more than 240mm of rain fallen in the Aorere Valley in the last 30 hours.
Some Golden Bay residents are leaving their homes. Water has risen quickly on Wednesday morning and while there are no mandatory evacuation orders in place, some people are choosing to leave.
Pohara's Thomas Cox was moving items to his in-laws down the road. It was the second time there had been flooding since Waitangi Weekend.
"So everything is saturated and nothing is taking water, it's all just going out," he told 1News.
There are some road closures, which can be found on the NTEM Facebook page.
Parts of Buller and the West Coast have a red warning in place.
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