And part of the solution will be to clean more than 2,500 kilometres of water pipes.
The Winnipeg Regional Health Authority says the level of manganese in the city’s water supply is not harmful.
Diane Sacher, the city’s director of water and waste, says there is much less of it in a glass of city tap water than in other beverages.
She says a cup of apple juice has 10 times the level of manganese seen in Winnipeg water, while coffee or tea can have 20 times the level.
Nevertheless, the brown water is unappealing to residents and Mayor Sam Katz says the city will work on fixing the problem.
The report by a environmental and engineering consulting firm says some of the manganese in the water system comes from Shoal Lake but the main source is the water treatment plants, where it is used as a coagulant.
“We add it to water so that it helps clump algae and other organic material together so that it’s easier to remove," says Sacher.
The city says will find ways to reduce the amount of manganese used during the water treatment process, and then, beginning in May, it will begin cleaning the pipes.
It would usually take six years to do that but the city says the process can be finished in two years.
All that doesn't mean the brown water will entirely go away, especially during the summer. But the city says it hopes to bring occurrences of brown water back to 2008 levels.