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.
The European Environment Agency (EEA) said that water quality at 96.1 percent of the 21,000 bathing spots covered by its 2015 bathing water survey was at acceptable levels, which was a rise of 0.9 percentage points from 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. By contrast, only 56 percent of sites had reached that level in 1991.
"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 nearbybeaches," 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".