Fribourg cantonal police said emergency crews responded to 27 emergency calls, primarily for flooded basements in the Sarine area.
The communities of Treyvaux, Ependes, Le Mouret, Marly, Givisiez and Chiètres were among those impacted, police said.
Nine fire brigades helped deal with the high water.
Local fire fighters cleared a landslide that covered the Route du Condoz in Villars-sur-Glâne, cantonal police said.
As a precaution due to unstable rock in the area, police closed the road to traffic overnight with a diversion put into place.
No injuries were initially reported.
The rain followed storms on Sunday that swept across a region extending from Vaud to Lake Constance.
Hailstones pummeled the vineyards of Morges and Lavaux in the canton of Vaud, insurer Schweizer Hagel (Suisse Grêle) said.
The insurer said hail also fell on the cantons of Fribourg, Bern, Basel-City, Basel-Country and Aargau.
The company said it received claims from 700 market gardeners, fruit growers, wine growers and horticulturists who suffered damage estimated at up to three million francs.
The cantons of Jura, Neuchâtel and Ticino were among those also reporting heavy rain, the ATS news service reported.
Meanwhile, winds close to 100 kilometres an hour were clocked in Schaffhausen and 90 km/h in Basel.
MeteoSwiss is forecasting a drop in temperatures in most parts of Switzerland on Tuesday with rain across the country and thunderstorms in the southeast.