Flinders Shire Council says it is flushing out its water after numerous complaints from locals.
"Over the next few days you may notice that your water is brown," Council said on its Facebook page on Thursday.
" This is due to our Water and Sewerage Crew working their way through a main flushing program."
Parts of town have had brown water for a month or so after Council began increasing chlorine levels to comply with health guidelines.
Council said it would map the problem areas so that they can undertake a targeted and intensive scouring and sanitising regime.
"Those areas affected will be notified prior to this occurring as the mains will be shut off during cleaning," Council said.
Flinders Shire mayor Jane McNamara told ABC she hoped liquified chlorine would improve the situation instead of the granular chlorine previously used.
Earlier local businesswoman Sherilee Honnery said she had been battling with water issues in Hughenden for several days.
"I heard last night on the grape vine there is only around 10 people complaining about the water issues..... I know this is wrong," she said on social media.
"If you are having problems with the water or the chlorine in it PLEASE report it to council, yes you will probably get the same response and excuses I got, but if you don't put in an official complaint .... then that is all council will count.
She advised people to put in a complaint ring 4741 2900 and ask for it to be put through the CRM system or email email@example.com.
Ms Honnery said her complaint was not about council bashing but simply wanting to get action on the problem.
"If you do not make a noise then forever stay silent and just put up with it," she said.
Council offered tips if the tap water is discoloured:
- Run taps for a period prior to use (until water runs clear)
- Flush taps at your home - use water on your lawn or plants
- Clean out any build up in and around your tap head
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