Shellfish gathering was also not recommended over the next few days, said Thames Coromandel District Council operations manager Greg Hampton.
The wastewater overflows in Onemana and the Moana Point area of Whangamata Estuary, he said.
Signs have been put up to alert residents and visitors.
A shellfish ban has already been place for the area for over a year due to shellfish toxin levels in the Bay of Plenty, where the regional council is continuing to monitor river levels across the region with two rivers still to peak later today.
Community relations manager Bronwyn Campbell said the Whakatane River was still rising and was forecast to peak around 10pm at about a 30-year event level.
That was similar to Monday's peak for the river following last weekend's storm.
"We're also expecting that the Waimana River will peak at 6pm today at about a 50-year event level," Ms Campbell said.
Boaties were also being asked to take extreme care when out on waterways and along the coast this weekend.
"Swollen rivers have brought logs and debris down into the regions coastal waters including Tauranga Harbour, Whakatane River mouth, Ohiwa Harbour."
The District Health Board has warned that people should also avoid swimming and recreational contact in all rivers, streams and harbours for 48 hours as farm runoff may have contaminated them with effluent.
There have been a number of sewage overflows reported into Tauranga Harbour so people are advised to avoid contact with the water until further notice.
Meanwhile, the NZ Transport Agency said State Highway 1 through the Dome Valley between Wellsford and Warkworth, north of Auckland, would remain closed for several more hours because of flooding.
People travelling between Northland and Auckland are being diverted on to SH16 between west Auckland and Wellsford.
Flood waters are covering SH1 around the Hoteo Bridge at the northern end of the Dome Valley says the NZTA's state highways manager for Auckland and Northland, Tommy Parker.
"The flooding has been severe and waist deep in places, and the NZTA will not re-open the highway until it is satisfied that it is safe for drivers to use again," he said.
In Northland, a low-lying section of SH11 between Kawakawa and Paihia in the Bay of Islands remains closed by floodwaters. While most other highways and roads in the region have re-opened, the NZTA advises that damage and surface flooding are still making driving conditions hazardous and roads are restricted to one lane in several places.
There are also a number of slips on roads around the Coromandel Peninsula.
Former tropical cyclone Wilma is now well clear of the North Island, heading quickly out into the Pacific Ocean.
Apart from the Chatham Islands the system no longer posed a threat to the country, said Weatherwatch.co.nz weather analyst Philip Duncan.
However, strong winds in her wake were now pushing across the nation. Gale or near gale winds were affecting exposed parts of the Far North, Auckland, Taupo, East Cape, Gisborne, Hawke's Bay, Taranaki, Wanganui and Manawatu, he said.
In the South Island near gale winds were also pushing into exposed parts of Canterbury, the West Coast and Southland.
The northern part of the North Island is this afternoon cleaning up in Wilma's wake, which raised fears for two people believed missing after their house broke to pieces sliding down a bank and onto the beach at Onetangi, on Waiheke Island, this morning.
They were found safe and firefighters also had to use a boat to rescue a man and woman stuck up trees in Pipiwai, 43km northwest of Whangarei.
Around 70 people from Kaeo through to Kawakawa were evacuated overnight, however residents from Kawakawa are returning to their homes as the floodwaters recede.
About 280mm of torrential rain fell in the eastern hill country of Northland over 12-14 hours from 1pm on Friday, causing substantial damage to the region's road network and some water and sewage treatment plants.
Wilma's wet legacy saw Mt Maunganui, near Tauranga, closed to the public until Wednesday after severe mud slides and landslips following torrential rain made the area unsafe.
- NZPA
