One hundred and thirty beaches were deemed excellent, good or of satisfactory standard. However six failed to meet the legally required minimum standard.
Three of the six were in Dublin at Merrion Strand, Loughshinny, and Portrane and three in Galway at Clifden, Trá na Forbacha, and Ballyloughane.
Sewage and drainage misconnections, as well as septic tank discharges, contamination with dog and seagull faeces, and river inputs were the causes of the failures.
Dublin and Galway local authorities are now obliged to advise the public not to swim at those locations this summer.
The Environmental Protection Agency said the public can help by taking their rubbish home from the beach, and bagging dog poo rather than burying it in the sand.
140 beaches are continually tested by the EPA for bugs that can cause a sick stomach, a respiratory illness, or swimmers itch.
The EU sets the standards and the tests are twice as strict as they used to be.
Speaking on RTÉ's Morning Ireland, EPA Senior Scientific Officer Peter Webster said there are still 43 areas of concern from around the coastline where raw sewage is pouring into the sea.
He said, fortunately, not many of them are near identified beaches, with the possible exception of Youghal.
Mr Webster said the intention of Irish Water is to spend around €350 million between now and 2020 to address issues.