Dollymount Strand in Dublin has lost its blue flag status just one year after it won the award for the first time.
Tests of the water showed it to have been slightly contaminated by effluent and while it met minimum standards for bathing water, it failed to meet the higher standard for blue flag status.
In total 83 beaches and marinas in the Republic were granted the award. This is one less than the record number awarded last year.
Eight beaches in Northern Ireland were also awarded blue flags in a similar scheme, administered by the charity Tidy Northern Ireland.
This is the same number as last year, with one new addition, Portrush East Strand. Downhill beach in Co Derry was removed from the list.
Co Kerry and Co Mayo again topped the list of blue flag winners in the Republic, with 13 each. Donegal was next on the list with 11, while Co Cork held on to 10 of its blue flags.
Five beaches including Dollymount and Malahide in Dublin lost the award, while a further three regained flags previously lost.
Other beaches to lose flags were Enniscrone in Co Sligo, Culdaff in Co Donegal and Doonbeg in Co Clare.
There was just one new flag, for Céibh an Spidéil in Co Galway.
The loss of Dollymount's flag was seen as particularly disappointing as Dublin was the only capital city in Europe with a blue flag beach within its boundary.
It gained the blue flag following the opening of the sewage treatment facility in Ringsend, which removed most of the poorly treated waste from Dublin Bay.
Yesterday a spokesman for Dublin City Council, which is responsible for the beach, said it had discovered the possible source of the pollution being blamed for the loss of the flag.
Engineers believe it was a malfunctioning effluent treatment plant in north Dublin on the outskirts of the city, and new measures have been introduced to prevent similar problems.
To receive a blue flag, beaches must meet and surpass a range of criteria, including water quality, facilities, cleanliness and safety. New criteria added this year include the requirement for recycling facilities at the beaches awarded blue flags.
Announcing the awards yesterday, Minister for the Environment Dick Roche said that bathing water quality in Ireland continued to be among the best in Europe. He said 97 per cent of bathing water in Ireland complied with minimum European standards and 90 per cent with the higher blue flag status.
However, both Mr Roche and An Taisce, which oversees the blue flag scheme in the Republic, highlighted the ongoing problem of littering and animal faeces as a serious threat to many of the beaches.
In a statement announcing the awards yesterday An Taisce warned that "some bathing areas are subjected to tremendous pressure due to vandalism, littering, human-caused dune destruction and other impacts".