Emerson's Brewery manager Chris O'Leary said it was hoped production might resume tomorrow.
However, potential customer growth would be limited next month by the lost productivity from this week.
"We have got plenty of stock," he said.
"But any stock we have got will be sold in the month we make it."
The loss of productivity could cost the company as much as $60,000, though that number was based on "gut feel".
Reports the company had to dump stock were incorrect, as Monday and Tuesday's output remained in quarantine ahead of the results of testing.
He hoped the council would take into account the business losses stemming from the "mistake'' going forward.
"In the future I'd like this taken into account when we are dealing with the council," he said.
"They might compensate - not in concrete [cash amounts], but next time we are dealing with them maybe they can help us [businesses] out."
Mr O'Leary said production had been halted at the facility, all water drained and several batches of beer held in quarantine while awaiting test results.
''We have drained all the water from every spot in the brewery,'' he said.
''We are waiting on the all-clear from the Dunedin City Council before we bring water back into the brewery.''
None of Emerson's beers were pasteurised, but it was unclear what effect the tainted water would have had on brews.
''That ... might take care of [pathogens], but we wouldn't want to take the risk,'' Mr O'Leary said.
''No matter what happens, the quality of the water is the most important thing in brewing beer.''
Despite the disruption to production, there was ''plenty of stock'' to survive the notice period and it had been a ''brilliant exercise in managing crisis''.
''The safest liquid to drink is beer in a crisis,'' he said.
Central city supermarkets returned to normal yesterday.
A Foodstuff spokeswoman said production of fresh food at Centre City New World had resumed after the store obtained access to fresh water from a large tanker.
It was limiting its sales of bottled water per customer ''to ensure there's plenty to go around''.
Countdown spokeswoman Kate Porter said the Ministry for Primary Industries had advised Countdown there were no concerns with baked goods.
''Our produce has not been washed or sprayed with any of the affected water and so we have plenty of fresh fruit and vegetables available,'' she said.
''Our Dunedin team is working hard to ensure that we have plenty of bottled water on our shelves.
''Obviously there has been an increase in customer demand today and whilst we are running low this afternoon on single bottles of water, we have plenty of larger packs of water.
''Additional supplies are being brought in from from Christchurch and Auckland.''
Many cafes and coffee outlets found ways of working around the problem, including using industrial dishwashers and pumping water into espresso machines from containers.
However, some small businesses closed yesterday and others were limited in what they could serve.
Sargoods owner Abby McErlane said the lack of water meant she could not make coffee, which was costing her $200 to $500 a day.
She did not have loss of income insurance due to its cost.
''It's quite expensive ... and we only bought the business in April and it wasn't something we thought we would need - but clearly it was,'' she said.
Mondelez spokesman Jake Hatton said the Cadbury factory's entire system had been flushed and it had increased its internal water testing programme and completed risk assessments on its manufacturing and cleaning processes.
