The agency's annual bathing season report, released on Wednesday, found that 134 of 210 bathing areas (61 percent) in Switzerland were of excellent quality based on sampling from 2014.
Two Swiss areas were found to have good water quality, while another two were judged to have the minimum requirements of the EU's bathing water directive for water quality, bacteria levels and public health risks.
Switzerland's four non-compliant swimming areas (less than two percent) put it slightly below the European average.
This year marked the first time the EEA included Switzerland and Albania in its study, along with the 28 member countries of the European Union.
A total of 21,000 bathing areas, including coastal beaches, lakes and rivers are covered in the report.
But complete sampling statistics for 34 bathing areas in Switzerland were unavailable, according to the EEA.
Another 42 places for swimming in lakes and rivers were classified as “new, changed or closed”.
The EEA's findings for Lausanne also do not jibe with information for 2013-14 from the international commission for the protection of Lake Geneva water (CIPEL).
According to its map of beaches on both the French and Swiss sides of the lake, none are classified as having bad quality water for swimming.
CIPEL said that the water quality at Le Flon and the Plage de Bellerive in Lausanne was “good”.
The quality was “average” at other Lausanne beaches at Le Parc Bourget and La Vaudaire, it said.
The commission warned bathers to take showers after swimming at two areas of the canton of Geneva (Port-Gitana, Bellevue and Pointe-à-la-Bise, Collonge-Bellerive) where the water can be “temporarily polluted”.
The European study found three countries — Cyprus, Luxembourg and Malta — had excellent water quality in all of its public bathing areas.
The countries with the greatest number of areas with poor water quality were Italy (107 sites), France (105) and Spain (67).
For more information about the EEA study, check here.