Sewage water from the Lower Molonglo wastewater treatment plant spilled into the Molonglo River overnight.
Residents are being asked to not draw water from the river or go swimming in the next few days from the junction of the Molonglo River and above Burrinjuck Reservoir.
Icon Water, which operates the waste plant, said the water was "partially treated" and said the spill was caused by heavy rain over the weekend.
"Some spilling from our bypass storage dam may still occur over the coming days," said Icon Water in a statement.
"We continue to process the inflow following the 50mm of rainfall across the Canberra region over the weekend.
"The majority of effluent discharged from the plant continues to be fully treated and fully disinfected."
The company said the flow of water represents less than two per cent of the Molonglo River flow and less than one per cent of the Murrumbidgee River flow.
"There is no risk to the ACT water supply as the effluent is released downstream. ACT residents can continue to use their taps and drinking water as usual," Icon Water said.
"Icon Water has notified both the ACT and NSW Environment Protection Authorities (EPAs), ACT Health and close by residents affected by the discharge."
For further information, please call Icon Water's faults and emergencies line on 02 6248 3111.
