Whanganui District Council declined the Chronicle's request for an interview, but confirmed in a statement they had received 14 complaints from residents in recent weeks.
"Discolouration is usually caused when a section of water main is shut-off for repairs and/or renewals. Reinstatement of the water main can then result in discolouration to the water supply," senior engineering officer Dave Rudolph said.
"The replacement of a large section of water main on Hillside Tce that feeds into the Aramoho, Whanganui East and Durie Hill areas is the possible cause of these water-quality issues."
But Rudolph said the cause could also be naturally occurring substances within the city's infrastructure.
"Another possible cause of the discolouration is naturally occurring sediments that settle at the bottom of the water supply lines. If water velocities increase because of a break to a water main, leaks and varying water pressures can stir up the sediment and cause discolouration."
According to posts on social media, discolouration appears to be most prevalent in the eastern suburbs of Whanganui, including Aramoho, Whanganui East and Durie Hill.
"We've been having it every few days for weeks," one resident said on social media. "I'm in Durie Hill - water is yellow and brown all the time," another said.
Following the Chronicle's queries, the council posted on Facebook saying that it would be working to flush pipes around the affected suburbs.
"Please be aware that we will be flushing water mains in the Whanganui East, Bastia Hill and Durie Hill areas. This will continue until 4pm on Friday, May 28," the post said.