Effluent will be discharged into the Molonglo River on Sunday after heavy rainfall infiltrated the sewerage system.
Icon Water said the Lower Molonglo Water Quality Control Centre treatment plant would discharge a small amount of partially treated effluent into the river between about 11am and 12pm.
"The majority of the flow that will be discharged will continue to be fully treated and fully disinfected, with a small portion of partially treated effluent that is not fully disinfected," the ACT's supplier of sewerage services said in a written statement.
Icon Water advised residents on the section of the Murrumbidgee River from the junction of the Molonglo River and above Burrinjuck Reservoir not to draw water from the river for either potable (drinking or food preparation) or non-potable (domestic or stock watering) purposes for the next 48 hours.
It also advised against swimming and other sports involving bodily contact with the water in that section of Murrumbidgee River over the time period.
Icon Water said there was no risk to the ACT water supply and that residents can continue to use their taps and normal drinking water.
It had notified both the ACT and NSW environment protection authorities, ACT Health and residents living nearby that may be affected by the discharge.