Up to 40 millimetres of rain was forecast overnight on Wednesday and into Thursday morning, with up to 80 millimetres forecast in the Hohe Tauern, according to the Central Institute for Meteorology and Geodynamics (ZAMG).
The areas in Salzburg most at risk of floods and mudslides are Pinzgau, Pongau and Tennengau.
The heavy rain could see some rivers reach the warning limit and local authorities have advised residents to avoid unnecessary journeys and walks.
Residents have also been told to keep windows on the ground floor and in basements closed, and to seal basement shafts.
Weekend weather forecast
From Thursday afternoon, there should be a break in the weather as the heavy rain is expected to ease. There is even some sunshine forecast for the west of the country.
On Friday, showers are forecast in the north of Austria while the south is expected to stay dry with intervals of sunshine.
The forecast for the weekend is mixed with sunshine for most of the country on Saturday, followed by a cold front on Sunday and a possible thunderstorm for the south side of the Alps.
There are strong wind gusts forecast for the Danube region on Sunday.
A summer of extremes
So far, the summer season in Austria has been a mixture of extremes with high temperatures followed by storms and heavy rainfall.
Between June 16 and 29, the ZAMG recorded temperatures of more than 30 degrees for most of the country. In some places, temperatures reached up to ten degrees above the long-term average for June.
Then in July, storms and heavy rain hit Austria, resulting in flood warnings for rivers in Salzburg and Tyrol and helicopters deployed for rescue operations.
The Kurier reports that the recent hailstorms in Tyrol, Salzburg and northern Burgenland were some of the most costly on record in terms of insurance claims.