The city, which has a population of about 700,000, said the move was precautionary after six water samples showed the presence of E. coli and coliform at extremely low levels.
"Out of an abundance of caution, we are issuing it citywide," Mayor Brian Bowman told a hastily called news conference Tuesday evening.
"Hopefully we will find out that these were false positives tomorrow and very soon thereafter we will be able to lift this notice, but we do need to be cautious."
Melissa Hoft, a spokeswoman for the Winnipeg Regional Health Authority, said in a release there was no information to suggest there had been any increased illness attributable to the drinking water.
"Common symptoms associated with waterborne infection include gastrointestinal symptoms, such as nausea, vomiting and diarrhea," she said.
"Most people who are affected by a waterborne illness would be able to recover at home. A sign to be concerned about would be the presence of bloody diarrhea and dehydration, and people having either of those symptoms should seek medical attention."
Hoft said hospitals in the city had activated contingency plans.
Surgeries would not be affected since all procedures are done using medical-grade water supply, she said.
"While hemodialysis does use the city water supply, the reverse osmosis process of dialysis filters all bacteria and potential contaminants, including E. coli," she said in the statement. "This process is safe."
As for other patients, signs had been posted at water fountains advising not to drink the water and staff were ordering bottled water for patient and staff use.
Throughout the city, residents were told to bring tap water to a boil for at least one minute before using it to drink, make food or infant formula or brush teeth.
But it is not necessary to boil tap water for other household purposes, such as laundry or washing dishes.
Adults and children who can avoid swallowing water can use it to bathe. All commercial buildings, public and private, including restaurants, daycares and rest homes, are under the boil-water advisory.
All city pools remain open and the city says they are safe to use. The Pembina School Division said schools would be open today, but asked parents to send bottled water with their children as the water fountains would be shut off.
Adam Schinkel, co-owner of Water World, a bottled water company, said his stores had closed for the day when the news broke.
"I got home around six o'clock, my phone started to blow up and all I was told was there was a boil-water advisory issued citywide in Winnipeg," he said.
Schinkel said he started making calls and staff at the stores quickly headed back to reopen.
"Our phones are ringing off the hook and we have a steady stream of customers coming in," he said. "We're here to help people that do need the water. From what I'm hearing, a lot of the grocery stores are already sold out of bottled water, so that's sort of where we come into play."
However, Dave Bilyk, a homeowner in south Winnipeg, said his family was coping well and did not feel the need to rush out and buy bottled water.
"We boiled about five or six litres worth and that way we can run it through the Keurig (coffee maker) for coffee in the morning and we can use it for brushing our teeth and so on."
He said the only hiccup so far is the fact his daughter does not fully trust assurances that the water is safe to bathe in. His son, however, feels differently.
"I think she's skipping a shower cause she's not convinced the water is really clean," he said with a chuckle. "The boy didn't have a problem but the girl does."
City officials said the water samples were part of routine testing and were collected Monday at 39 public locations. The results became available on Tuesday.
Geoff Patton, acting director of the Water and Waste Department, said the results are puzzling, adding some showed the presence of both coliform and chlorine. He said those two don't go together and it suggests the samples may be "false positives," or incorrect indications of the presence of bacteria.
"It's hard to understand — we see clean results upstream and downstream of the locations, and then we see this unusual sampling. So what has happened? That is what we're looking to do. We've taken additional samples this morning that were distributed through the entire city and we're expediting those samples to make sure everything is safe."
The health authority said the presence of chlorine was "reassuring because this would suggest that any bacteria or viruses present in the water would likely be killed."
Officials didn't specify what type of E. coli was found in the samples. The presence of E. coli in water indicates recent fecal contamination and may indicate the possible presence of disease-causing pathogens, such as bacteria, viruses, and parasites. The Canadian Drinking Water Quality Guideline for total coliforms is zero per 100 millilitres of water and zero for E. coli.
Patton said the results of the samples included many with one coliform-forming unit per 100 millilitres and one that was higher, possibly nine.
While five of the six positive tests were east of the river, one was in the city's southwest and Bowman said that led the city to expand its warning.
"This is a public health issue, this is the City of Winnipeg's water supply, we're confident in the safety of the water and we're resampling to prove this out," Patton said.
The city has faced water problems before. In 2013, a boil water advisory was issued and later lifted for a neighbourhood in Winnipeg when it was determined there was no E. coli contamination.
However, the city and province faced hard questions about how people were notified.
The province had issued an advisory five hours after the chief provincial public health officer said he had been aware of the positive test results. The city blamed the delay on Manitoba Health and said once it knew what was happening a news release was immediately issued.
Provincial officials said it took that long to determine a course of action.
Then about a year ago, the city finally figured out the cause of brown water that had been periodically pouring from residents' taps for months.
They blamed manganese from Shoal Lake and water treatment plants, where it is used as a coagulant.
Then-mayor Sam Katz admitted the brown water was unappealing to residents and said that although health officials said the levels of manganese were not harmful, the city would nevertheless clean more than 2,500 kilometres of water pipes.
The city also said it would find ways to reduce the amount of manganese used during the water treatment process.
Winnipeg's water is piped from Shoal Lake, Ont., about 150 kilometres east of the city, and treated at a plant near the Decon Reservoir east of the city. The $300-million facility opened in 2009 and can treat up to 400 million litres of water a day.
Seven people died and thousands were sickened in Walkerton, Ont., in May 2000 when E. coli got into the water system. An inquiry found cost-cutting by the government of former Tory premier Mike Harris contributed to the tragedy.