The beaches that failed the test are centred mainly on the Stockholm region and Skåne, with two popular bathing spots in central Stockholm deemed not to be clean enough.
Overall, water quality in Sweden was viewed as good by the EU report, released on Thursday. Some 96.8 percent of Swedish coastal beaches had acceptable water quality, which 95.9 percent of beaches on freshwater lakes passed muster.
Eleven coastal beaches and six lake beaches were given red marks by the survey, compared to eight and three respectively last year.
The list was based on readings taken last summer, but European officials are recommending that people use the lists when deciding where to bathe this year.
The beaches to be failed included Ängbybadet in Bromma, western Stockholm, and Smeduddsbadet on Kungsholmen. In western Sweden, only Björkäng near Varberg failed the tests while ten beaches in Skåne were given red marks. These included all beaches in Trelleborg.
Anneli Carlander at the Swedish Institute for Infectious Disease Control told Dagens Nyheter that the readings did not always give a full picture of the water quality in a particular area. She recommended visiting her organization's website for up-to-date readings from Swedish bathing areas (website in Swedish).