Lake Burley Griffin will be closed for at least a week after heavy rains caused partially-treated sewage to flow in the to the lake from Queanbeyan Sewage Treatment Plant.
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Hazard warnings have been issued about swimming in the lake or having any contact with the lake water.
Icon Water says the recent rain also caused the treatment plant at Lower Molonglo Water Quality Control Centre to is discharge partially treated effluent into the Molonglo River.
"The majority of the flow being discharged is fully treated and fully disinfected, with a small portion of partially treated effluent that is not fully disinfected," it said in a statement.
"Icon water advises 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. We also advise against swimming and other body contact water sports in this section of Murrumbidgee River over this period."
It said there was no risk to the ACT water supply, but it had notified the Environment Protection Authority and ACT Health.
Meanwhile, ACT Environmental Protection Agency advice indicated the Queanbeyan plant went into "diversion mode" at close to midnight on Friday after rainfall inflows exceeded the plant's normal operational capacity.
National Capital Authority Peter Beutel said the closure of Lake Burley Griffin would be in place until at least September 9 and the public were urged to wash their skin with soap after contact with the lake waters.
"There is the potential for partially treated sewage material to be in the lake," he said.
He said during normal processing, liquid materials would be fully treated and flow into the Molonglo River and then on into Lake Burley Griffin.
However the heavy rain event disrupted this.
"It is getting treated less - it's not getting the full complement of treating. It abbreviates the full round of the process of treatment."
He said the high volumes of rain meant any hazard effluent was highly diluted and the risk to human health was deemed low.
The Scrivener Dam also went into flood operations at midnight on Friday.
At its peak there was two 200 cubic metres of water per second being released. From 2.30am to 10am Saturday, two gates were opened to deal with the deluge, however as rain eased on Saturday there was only need for one gate to be open.
Flood operations at Scrivener Dam are typically put in place twice a year.
