Unlike real tornados, however, waterspouts can form in weak winds, said Swiss weather office SRF Meteo, which reported the sighting.
At the time the waterspout was seen, winds in the area were between ten and 23 kilometres an hour.
This natural phenomenon forms when layers of instable cold air make contact with a body of warm water, said SRF Meteo.
The cold air heats up over the lake and starts to rise. Depending on the wind conditions, this rising air starts to turn, accelerating to form a whirlwind.
On Saturday morning the temperature of Lake Zurich was 22 degrees, said SRF Meteo, while the air temperature was around 13 degrees.
Though rare in Switzerland, waterspouts like these are mostly seen at this time of year when autumnal air temperatures combine with warm water.
The country experienced a distinct autumnal feel over the weekend, with ground frost at low altitude for the first time since the spring, said MeteoNews.
Temperatures fell to around zero in many places, with -1 in Zurich-Kloten, -0.6 in Sion in the canton of Valais and -4 in La Brévine in the Jura, known as the coldest place in Switzerland.