Spain, which boasts 10.1 percent of all bathing spots in the European Union recorded 1.821 bathing spots that were rated excellent, representing 83.2 percent of the total.
But Spain was also the nation identified with the third highest number of sites with poor water quality in the report published on Thursday.
The EEA identified 58 bathing spots that failed to meet the minimum quality, the third highest figure after France (95) and Italy (58).
"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 farmsand farmland," it added.
For an interactive map of the state of Europe's bathing waters, click here.
Spain broke its own records this year with a total of 586 blue-flag beaches - the highest mark of a beach's cleanliness and environmental friendliness, the Association for Environmental Education and the Consumer (ADEAC) announced in a report earlier this month.
This was up from 577 last year and meant that Spain was once again the top country worldwide for blue flags - a place it has held for nearly three decades since the awards began in 1987.
This also means that one out of every six top beaches in the world are in Spain, and one out of every five Spanish beaches will be flying the blue flag this summer, according to ADEAC.
Wherever you are in Spain you will not be far from an excellent rated bathing spot.