Numerous rivers and lakes spilled over their banks over the weekend as more than 20 centimetres of rain fell in eastern Switzerland starting on Friday.
Meteonews said Amden, a municipality in the canton of Saint Gallen, received as much as 25 centimetres over the weekend, a record for the country.
The rain subsided on Sunday but water levels in lakes and rivers remained dangerously high in various locations.
In the capital city of Bern, emergency workers placed barriers along the Aar River to minimize flooding, the ATS news service reported.
In the canton of Lucerne, a landslide in Werthenstein closed a rail line west of the city of Lucerne.
Mud and gravel buried sections of rail ines in the canton of Zurich between Rütli and Jonas (Saint Gallen) and also at Wald in the Töss Valley, ATS said.
Flooding of the Greifen and Pfäffikon lakes, in the canton of Zurich, was also reported, while the Rhine flooded its banks in Basel and elsewhere.
Various other lakes such as Constance, Zurich, Lucerne and Walenstadt were expected to see their levels to rise to a peak level late on Sunday, said MeteoSwiss, the national weather office.
Meanwhile, the heavy precipitation forced the closure of several mountain passes.
The Gotthard Pass closed on Saturday because of avalanche risks, Viasuisse said in a press release.
The San Bernadino pass in the canton of Graubünden closed due to snow, along with the Jaun pass in Fribourg.
Another landslide in the Oberalp pass in Uri closed the road, ATS said.
The rain was caused by a depression coming from Poland which hit eastern Switzerland early on Friday.
Western Switzerland was largely spared the heavy rain, although the northern Jura region and the Fribourg pre-Alps were exceptions.
MeteoSwiss said the worst affected areas of the country received between five and ten centimetres of rain from Friday morning until Saturday afternoon.
Snow fell in mountain regions above 1,600 metres, the national weather office said.
The persistent rain followed a wetter than usual May with less sunshine than average in many part of Switzerland.
The full extent of the damage caused by the flooding is not expected to be known for several days as cantons assess the situation.
Meanwhile, the forecast calls for warmer weather through this week, although thunderstorms are expected in many regions on Wednesday and Thursday.