The Poroti plant was completely flooded leaving all pumps underwater. Venmore said they need to be either replaced or dried out and repaired which would take "several weeks".
"Effectively that treatment plant is no longer useful for the short term."
Meanwhile, the debris which washed into the Whau Valley Dam during the downpour - turning it into the colour of the Hātea River -meant the Whau Valley Water Treatment plant struggled to cope with quality of the water.
Venmore said they had to shut it down temporarily and bring it back online slowly which took all of yesterday and into the night. It was finally brought back online at low flow about midnight and teams worked until 6am to bring it back to a normal flow.
With the plants out of action, water from reservoirs was being used causing levels to drop dramatically - the main reservoir at Fairway Drive dropped down to 13 per cent last night.
"Normally they would be full or nearly full but once the treatment plant shuts down, people are still using water so they're using water out of those reservoirs. They draw it right down and normally we just top them back up but we couldn't.
"They're all really low at the moment and we're trying to get more water in them. That's why we're needing people to save water because if we can't save more water than we're producing, we will run out."
The Paihia Water Treatment Plant - which was damaged in the deluge - is also now back in operation following successful provisional repairs overnight.
Work on a temporary pump and additional pipework was completed by contractors at 9pm yesterday and plant operators finally left the site at around 3am, satisfied the water treatment plant could meet demand.
Far North District Council infrastructure manager Andy Finch said the priority now was to recharge storage reservoirs to ensure backup supplies are available.
"I want to thank households and businesses for reducing water consumption yesterday. This helped get us through the immediate crisis.
"However, we still need all those connected to the Paihia supply from Waitangi to Opua to continue conserving water for the time being while reservoirs refill."
Finch said it will take at least two days for the reservoirs to re-charge, particularly the large Paihia reservoir.
Meanwhile, the Russell Wastewater Treatment Plant is no longer overflowing and the treatment plant is working at full capacity to meet demand.
"Yesterday's break in the rain significantly reduced stormwater infiltration into the system. As long as there are no further heavy rainfalls, the plant will continue to recover," he said.
The Council has spoken to the Northland District Heath Board about the spill and it is advising people not to collect shellfish or swim in the wider Uruti Bay area for at least five days.
It said all harbours in the district should be treated with caution following very heavy rains as waterways will likely be impacted by pollutants from various sources, such as farm runoff or private septic tanks inundated by flood waters.
