Bacteria of risk to public health has been detected in bathing waters deemed of good or excellent quality under European standards.
A team of researchers from NUI Galway released new research, which reveals the widespread contamination of some recreational waters over several years.
They published analyses on 111 samples taken from 50 locations in Galway city and county, Cork city and county and Fingal in Dublin between 2016 and 2019.
They detected a pathogenic form of E.coli called Shiga-toxigenic E.coli (or STEC), which can lead to potentially life-threatening infection in about 10% of cases.
The bacteria was detected in 57% of 84 sea waters where samples were collected - all of which are deemed of good or excellent quality based on current EU bathing water monitoring criteria.
STEC was also detected in 78% of the 27 lake and river samples tested.
Professor Dearbháile Morris is with NUIG's Antimicrobial Resistance and Microbial Ecology (ARME) team.
She told Newstalk Breakfast this could be coming from a number of sources.
"This particular type of E.coli can live in the guts of ruminant animals - so things like cattle, sheep and goats - but can potentially also live in the guts of humans if they happen to be infected with this particular organism.
"But it isn't natural to the guts of humans.
"Where it comes from potentially could be agricultural run-off, or it potentially could be sewage.
"The concern that we had is that under current EU bathing water quality monitoring criteria, they just look at our waters for the total number of E.coli that's present - they don't look at the characteristics of that E.coli."
Prof Morris said this could mean a Blue Flag beach could "potentially" have this E.coli.
"It's not that we're doing anything wrong or different in Ireland, we're adhering to the EU regulations, we're looking for E.coli in the waters - but we're not looking for the right thing, in my view.
"We should be looking at the characteristics of the E.coli.
"We did find in some cases that where the water was designated as of good or excellent quality under the current criteria, that we found these organisms in the water.
She said the regulations should be changed, but the public can help as well.
"We launched the Blue Spaces survey just yesterday... if you log on to nuigalway.ie/bluespaces - you can register and let us know why you interact with our blue spaces, and what might stop you from interacting with our blue spaces.
"And through that survey, everybody can help us to understand how we can improve our recreational water for the enjoyment of everybody".