A council spokeswoman said the discolouration could happen again during the next couple of weeks.
If it does, she advised residents to run the tap for 20 minutes to flush the system but to call the council's customer service team if the discolouration continued.
"This is part of our final testing and will carry on for a couple more weeks.
"Although the water source in these bores is low in manganese, the testing dislodged some silt in the line."
She said they received 65 calls on Wednesday and a few on Thursday morning about the discoloured water.
"There are no health risks associated with [it]."
Hospital Hill resident Glenn Marshall said he had to run his tap for two hours on Wednesday afternoon before his water returned to normal.
He said the council told him about the upgrades at Awatoto and that he should run a tap for 20 minutes.
Marshall said he thought the council should have notified residents in advance.
However, he acknowledged the quick work of council staff who came out to his street and helped flush the water network after he contacted councillor Keith Price for help.