The EEA also said that while extreme flooding washed more pollution into Central European lakes and streams of mainland Europe the overall water quality of beaches, lakes, and rivers improved across the continent last year, the agency said in its annual report published on Tuesday.
Some 95% of swimming sites in the EU met minimum water quality standards in 2013, up slightly from 94% in 2012, according to the agency, which provides scientific data to guide policymakers.
Inland waters suffered because extreme flooding had funnelled sewage into lakes and streams, the report said. About 90% of inland sites met minimum quality standards, down slightly from 91% in 2012.
But around 97% of coastal waters met quality standards, almost steady with the previous year. Southern Mediterranean countries, who rely heavily on pristine seas to attract tourism revenues, had the highest rankings.
All of Cyprus's bathing sites were judged to be 'excellent' and awarded 100% , followed by in second place Malta (99%), third place Croatia(95%), and in forth place Greece (93%).
Meanwhile other nations continue to lag.
In Estonia, some 6% of bathing sites were of 'poor' quality, the lowest classification out of four, failing to meet EU standards.
Also at the bottom of the list was Netherlands and Belgium followed closely behind, with 4% and 5% respectively.
Germany was harder hit than Belgium by last year's flooding, the report said, but still managed to ensure 92% of its 2,000 inland water sites met quality standards.