But a thunderstorm warning remains in place for south-west Victoria.

The Warrnambool SES unit received 91 calls for assistance, while Hamilton had 21 and Portland 16 as of 5.45pm Saturday. The call outs were mostly for flooding and water entering buildings through ceilings.

SES south-west duty officer Bess Krause said flood waters in Warrnambool began to subside at 4.30pm.

"Looking at the radar we are in for some more rain, but the warning has been downgraded at this point in time," Ms Krause said.

The Port Fairy, Camperdown and Hamilton SES units assisted Warnrmabool during the weather event, while Heywood assisted Portland.

Update, 5pm: Warrnambool restaurant owner Bud Knackstedt spent the afternoon mopping up water that had entered his premises.

Water about an inch deep flowed into the Siamese Restaurant on Lava Street, leaving he and staff to squeegee and mop the venue before service tonight.

Mr Knackstedt said the water came from the flooded street underneath the restaurant door, after drainage at the heritage building was unable to cope with the intense downpour.

"We just had to try to stop the water as much as we can, and then clean up afterwards," he said.

Mr Knackstedt said there was no damage immediately visible and the venue would open tonight.

"We will see what kind of damage we have long term," he said.

He said the venue experienced similar flooding about six years ago

Update, 4.50pm: Precautionary flood gates along Russells Creek will protect against the potential for riverine flooding.

Warrnambool City Council said it would install the gates on Saturday afternoon "as a precaution" and pedestrians should avoid the Russells Creek footpath.

Water was across Queens, Whites and Botanic roads, the council said.

Update, 4.10pm: The Bureau of Meteorology says rain in Warrnambool on Saturday has met its threshold for one-in-50-year intensity.

BoM forecaster Christie Johnson said 30 millimetres of rain fell in about 12 minutes.

"That is pretty intense, that meets our threshold for a one-in-50-year rain intensity," Ms Johnson said.

She said the chance of rainfall as intense occurring in Warrnambool every year was just two per cent.

"That means on average it will happen once in 50 years, the threshold is 19.8 millimetres in 10 minutes, or 24.1 millimetres in 15 minutes," Ms Johnson said.

She said 25 millimetres of rain fell in 45 minutes in Port Fairy and Dartmoor had 20 millimetres of rain in 15 minutes.

The rainfall has caused flash flooding.

"Flash flooding is very intense rainfall in a small location and tends to overwhelm whatever drainage system is available and causes temporary flash flooding," Ms Johnson said.

"It can come on very quickly and that's one of the reasons it can be quite dangerous."

Update, 3.40pm: Warrnambool SES units are responding to more than 60 incidents in the city following flash flooding.

Warrnambool SES unit controller Giorgio Palmeri said among the 60 incidents, crews had responded to reports of two people trapped in vehicles in floodwaters on Kepler and Wanstead streets, but no rescue was required.

"We got there after they were out of the vehicles," Mr Palmeri said.

Update, 3.17pm: Emergency services have issued a flash flooding warning for the Warrnambool area after more than 40 millimetres of rain has fallen on the city since 2pm.

The warning advises people to "immediately move indoors, away from floodwater".

"Do not enter floodwater," it says.

If you are inside:

If you are outside:

If you are driving:

EARLIER: Warrnambool streets have experienced flooding as heavy rain hit the south-west on Saturday afternoon.

North Warrnambool's Breton Street was inundated with water after heavy rainfall.

A resident of the street said the water was getting to a dangerous level and warned people to stay away.

SES south-west duty officer Bess Krause said earlier three houses in Port Fairy and one in Portland had called for assistance with water entering through the residences' ceilings.

"When we get this quantity of rain gutters can overflow and go into houses," Ms Krause said.

The Bureau of Meteorology issued a severe thunderstorm warning on Saturday afternoon, with rainfall, damaging wind, and large hail all possible.

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