Canberra's water supply will not be polluted by the spill, which was caused when the Lower Molonglo Water Control Centre treatment plant failed to cope with the weekend's deluge.

ActewAGL water division acting general manager David Glavas said about 1000 litres of partially treated effluent and 2000 litres of fully treated effluent was flowing into the Molongo River per second.

It was unclear how long the flow had been going for.

Mr Glavas said all of the flow was fully disinfected and ActewAGL planned to spend last night ensuring discharges returned to being fully treated.

The fully treated effluent has been through the primary, secondary, tertiary and disinfection stages of the treatment process.

The partially treated effluent has been through the primary, secondary and disinfection stages.

''The higher flows in the Molonglo and Murrumbidgee rivers will provide some dilution to the Lower Molonglo Water Quality Control Centre discharge,'' Mr Glavas said.

''Due to the wet weather that the ACT has experienced over the last few months, a high amount of ground and surface water has flowed into the sewer system, creating a higher inflow into the control centre.''

Mr Glavas warned that no water should be taken from the Murrumbidgee River downstream of the junction of the Molonglo River and above Burrinjuck Reservoir until Wednesday.

He also said swimming and any other contact with the water should be avoided.

The Lower Molonglo Water Control Centre is downstream of the sources of the territory's drinking water, so there is no threat to supplies.