The Federal Office for the Environment said there was a considerable risk of the River Rhine and Lake Constance bursting their banks.
The commune of Wallback am Rhein had to erect flood barriers as the river rose to within 50 centimetres of its bank.
In parts of the eastern canton of Graubünden and in southern Switzerland alarm levels were raised to the second highest level on Thursday as more rain was forecast.
MeteoNews reported that over 150 litres of rain per square metre had fallen in the past 48 hours in the southern canton of Ticino – the normal amount for one month.
In Robiei as much as 162 litres was measured.
In Graubünden up to 95 mm of rain fell and snow made a comeback at an altitude of 1,500 metres in Graubünden.
The canton's Flüela pass had to be closed overnight after a rockslide and several roads were blocked by landslides, the police said.
In the canton of St Gallen the fire brigade were called out 50 times to pump out cellars, but there were no reports of major damage.
In the northern cantons of Aargau and Solothurn too, the fire brigade were called out 20 times.
More rain is forecast over the weekend, with summer temperatures finally set to arrive by the middle of next week.