Wastewater treatment plants throughout Clutha are overflowing and there are reports of human waste in the district's floodwaters.
Clutha District Mayor Bryan Cadogan said the coastal part of the district was hit the most, and smaller catchments.
There was some flooding in Milton yesterday and a few commercial buildings in Balclutha had about a foot of water, he said.
"The district certainly flipped into recovery mode this morning," Mr Cadogan said.
"It's good to see a bit of sun.
"The teams are out assessing the damage."
Mr Cadogan said much of the heaviest rainfall was in Dunedin and the Clutha district was often not hit to the same extent.
"So we were very lucky that while we were getting a flick of the tail, we weren't receiving the full blast, more often than not."
The Clutha Mata-au River had not caused problems overnight.
Most of the district's sewerage plants were on flood plains and they had been inundated, he said.
A Clutha District Council spokeswoman said residents should assume all floodwaters are contaminated with sewage and chemicals and to avoid contact with floodwater whenever possible.
Wastewater treatment plants in Tapanui, Balclutha, Milton, Kaitangata, Waihola, Owaka and Kaka Point are all overflowing.
She urged residents to minimise their impact on the wastewater system by:
• Using alternative toilets: If you have a camp toilet or portable facilities, use these instead of flushing your regular toilet.
• Limiting flushing: Only flush if absolutely necessary to reduce the volume of water going into the system.
• Bagging toilet paper: Place used toilet paper in bags instead of flushing it, to prevent further stress on the wastewater system.
• Avoiding the use of water-heavy appliances: Refrain from using your washing machine, dishwasher, and other appliances that generate significant water runoff.
• Avoiding washing cars.
All transfer stations in the district are closed, including at Mt Cooee.
Clutha River levels began to drop Friday evening, having risen steadily since Thursday afternoon.
The country's biggest river by volume had passed its third flood-warning level with a flow of 1850 cubic metres per second, or cumecs.
Had it reached 2310 cumecs, that would have prompted a flood emergency warning.
But around 10pm on Friday, it peaked at 1940 cumecs, and has gradually dropped since then.
A state of emergency was declared in the Clutha district yesterday following the recent rain and flooding.
The Clutha District Council declared the state of emergency at 3pm after the flooding throughout the district overwhelmed emergency services.
Flooding has closed roads all over the district, both in and out of the townships.
State Highway 1 Waihola to Milton was closed overnight but reopened Saturday morning.
Multiple areas have experienced slips.
One slip on the Papatowai Highway closed the road and demolished a fence, leaving debris and sediment over the road and nearby paddocks.
Silver Fern Farms’ Finegand plant was preparing for the new season with their department inductions which were cut short due to flooding.
Their carpark was completely under water and workers were sent home.
By about 10.30am yesterday, Balclutha had received about 90mm of rain and it was still falling.
Rivers were extremely high and water was still travelling down from Central Otago because of the snow melt and extra rain.
The Clutha District Council advised people not to travel if they did not need to.
Civil Defence urged people to remain vigilant and treat floodwaters as though they were contaminated.
There was flooding across the region.
The Central Otago District Council issued a notice on its Facebook page saying that the Māniatoto and Manuherekia areas have been heavily affected.
River levels and creeks in these areas are beyond capacity and significant flooding was being experienced in many places.
The council has asked people to stay off the roads in these areas.
"If travel is essential expect to encounter flood waters, so reduce your speeds, and enter at a crawl speed."
Ranfurly residents were advised they could pick up sandbags from the Hazlett/Fulton Hogan yard "if needed".
More rain was expected in the Māniatoto overnight.
Civil Defence had not been activated in the Waitaki District, but the Community Centre is open for those seeking support or information.
Civil Defence Emergency Management (CDEM) has been supporting Council, contractors, Fire and Emergency New Zealand and police in over the past 48 hours.
They have been helping out particularly in and around Palmerston where State Highway 1 is closed between Hampden and Palmerston.
Road closures had been limited in Gore and Invercargill but the rain added to the dilemma Southland farmers have recently found themselves in.
Invercargill MP Penny Simmonds expressed her approval of an additional $50,000 in government support for farmers in Southland and parts of Otago yesterday.
"This funding will assist farmers and rural communities in our region, through organisations such as the Southland Rural Support Trust.
"The constant rain has affected the morale of farmers and their families, especially during calving and lambing season, which is already a demanding time."
Last month she said mid-September data from Environment Southland showed rainfall in some parts of Southland was more than 200% above the long-term average for the month.
