The State Emergency Service responded to more than 100 calls for help, while at least one car was abandoned to flood waters.

The deluge caused the ground floor of an apartment block in O'Connor to flood, with residents left to survey the damage to their soaked cars and belongings.

Bureau of Meteorology forecaster Rob Taggart said Sunday's rain was a once or twice yearly event in Canberra.

"There's been a trough sitting over western NSW for a couple of days, and that's drawn very humid, northerly air over the ACT. It's basically a tropical air mass," he said.

"What happened this morning was, a front has come through the south coast and it moved inland as a south easterly and it interacted with that humid air."

He said that collision produced a thunderstorm and the flash flooding.

Mr Taggart said the rain that fell over the capital on Sunday had exceeded the monthly average for February, which is 56.4mm at Canberra Airport.

Between 9am and 4.30pm, 50.2mm fell at the airport, on top of 19.6mm that fell on the previous 24 hours from 9am.

The northern parts of the capital copped the worst. Several roads were closed, some buildings were flooded and the ACT State Emergency Service received more than 100 calls for help mostly for flooding.

The rain fell hard and fast as people woke on Sunday morning.

In the three hours to 10.45am, the bureau recorded 66.2mm at Woolshed Creek, 43mm at Oaks Estate and 39.2mm at the boat harbour on Lake Burley Griffin.

In the 12 hours to 4.30pm, 78mm fell at Woolshed Creek, 55.6mm fell at Boat Harbour on Lake Burley Griffin and 59.2mm at Oaks Estate, the weather bureau said.

The Australian National University said in a statement that it had been forced to close the campus on Monday following floods.

"The closure is to ensure the safety of all students and staff as the University conducts essential safety checks on infrastructure including bridges, creek banks and electrical switchboards," the statement said.

"All classes and all events on campus will be cancelled on Monday 26 February and all ANU libraries will be closed.

"Students should not come onto campus, and residential students should stay away from affected areas."

As of Sunday afternoon, waterways and Sullivan's Creek continued to move rapidly.

The ACT State Emergency Service warned people to take care around flood waters and to avoid waterways.

"Do not drive into flood waters. If driving becomes too difficult pull over safely to the side of the road and wait until conditions improve," its statement said.

"The public are also advise to keep clear of waterways, which are likely to experience flash flooding in current conditions. When flooded waterways can become unpredictable and dangerous."

On Dickson's Morphett Street, a red Mini Cooper was abandoned in the middle of the road at the peak of the floodwaters.

Authorities had later moved it to the grass nature strip on the side of the road, where it sat with just one headlight on.

The waterway that runs through Lyneham and O'Connor became a rapidly flowing river and water nearly rose above the concrete edges.

Sullivan's Creek, which also passes through Turner, Lyneham and O'Connor, was overflowing and moving fast.

In a paddock off Majura Parkway, several horses gathered in the middle of the grass field, surrounded by water.

Authorities temporarily closed several roads, including Macarthur Avenue in O'Connor and Brigalow Street in Lyneham, but reopened them later on Sunday.

Oaks Estate low-level crossing and Majura Road from Tambreet Street to Mustang Avenue were also closed.

ACTION buses were diverted in the inner north for much of the day. Services returned to normal about 4pm.

The Bureau of Meteorology cancelled its severe thunderstorm warning about 1.20pm, after first issuing it about 9.15am.

But the rain has mostly passed, with the bureau forecasting only the chance of a shower coming into the new week.