In total, the European Environment Agency (EEA)'s bathing water quality report 2015 found 109 Swiss beaches to have ‘excellent' water quality.
Only three had poor water quality, said the report, two of them bathing spots on the Rhine near Kaiseraugst.
Beaches rated ‘excellent' were clustered around the lakes of Lugano and Locarno in Ticino, as well as the lakes of Zurich, Hallwil, Zug and the eastern end of Lake Geneva.
However the report doesn't give a complete picture, since some 101 Swiss beaches could not be properly evaluated because insufficient samples were taken or they were new last season.
Those included many of the beaches around Lake Geneva, Lake Neuchâtel and Lake Constance.
In last year's report three beaches in Lausanne, on Lake Geneva, as well as one in Kaiseraugst did not meet the agency's water quality standards.
But overall, Europe's beaches are getting cleaner and the vast majority of them met the EU's minimum requirements for water quality last year, the report concluded.
The water quality at 96.1 percent of the 21,000 European bathing spots was at acceptable levels, said the EEA, a rise of 0.9 percent on the previous year.
Across all of the sites monitored in the EU, Switzerland and Albania, more than 84 percent of the sites surveyed were rated excellent.
"European bathing water is at 96 percent acceptable and 84 percent excellent standards. That is the result of 40 years investing in water and waste water infrastructure," EU Environment Commissioner Karmenu Vella said in a statement.
The best swimming areas were in Luxembourg, Cyprus, Malta, Greece, Croatia, Italy, Germany and Austria, all of which had more than 90 percent of bathing sites rated excellent.
By contrast, only 56 percent of sites had reached that level in 1991, the EEA said.
"Several large tourist areas and cities like Blackpool, Copenhagen and Munich are... starting to benefit from investments in improved sewage systems, which are leading to cleaner bathing sites at harbour areas, urban river locations and nearby beaches," the agency said.
The highest number of sites with poor water quality were found in Italy (95), France (95) and Spain (58), according to the annual survey.
More than three percent of sites failed to meet the minimum quality standards in Britain (4.9 percent), Ireland (4.4 percent), the Netherlands (3.4 percent) and Bulgaria (3.2 percent), meaning they had the highest percentage of sites rated "poor".
"For recreational activities such as swimming, faecal contamination is a cause of concern for public health," the EEA said.
"The major sources of pollution are sewage and water draining from farms and farmland," it added.