Water in hundreds of rivers, lakes, estuaries, groundwater bodies and along Irish coasts is failing to reach acceptable quality standards.
The findings come from a new report from the Environmental Protection Agency (EPA) which assessed surface water quality between 2010 and 2015.
RTÉ reports that the findings have resulted in Ireland failing to meet its own national target for a 13% improvement of surface water standards during the six-year period.
The report concludes that overall there has been little change in water quality during the years of the study.
These failures cancelled out the improvements in quality in water bodies in different parts of the country.
The EPA said it recorded a continued and unwelcome decline in the number of rivers considered pristine, with just 21 reaching the mark between 2013 and 2015.
That compares to more than 500 in the late 1980s, it said.
"We now need to put the necessary measures and resources in place to arrest any further deterioration of water status and to make necessary improvements," said Dr Matt Crowe, Director of the EPA's Office of Evidence and Assessment.
"Decisions about what to do and who should do it and pay for it need to be based on scientific evidence and requires constructive engagement and collaboration across a wide range of stakeholders.
"By doing this, the right action can be taken in the right place by the right people and organisations."
A more positive sign was a continued reduction in the level of seriously polluted waters.
Just six rivers were designated as having bad water quality over the six years in question.
In comparison, 19 had the worst possible standards from 2007 to 2009.
Overall 91% of groundwater bodies, 57% of rivers, 46% of lakes, 31% of estuaries and 79% of coastal waters were found to have good or high quality water.
The EPA said a number of factors can influence water quality, but the main causes of pollution are nutrient losses from agriculture and domestic wastewater discharges, which can causes excessive growth of water based plants.
On the agricultural side the problem comes from nutrients like nitrogen and phosphorous as well as sediment running off the land and from farmyards into streams and rivers.
When it comes to domestic wastewater, the EPA said the problem lies with urban wastewater discharges, private wastewater discharges including septic tanks and a range of other sources including urban waste water misconnections.
Other pollution sources include forestry and extractive industry.
"While the national picture is relatively stable, some water bodies have improved while others have deteriorated, which highlights that not enough has been done to prevent deterioration of water quality," said Andy Fanning, Programme Manager for the EPA’s Office of Evidence and Assessment.
The EPA said the regions showing the most pollution are the south and south east with the western sea board recording the best results.
The report is the first full six-year assessment of the quality of our waters under the Water Framework Directive.
It requires good water status in all water in all but exceptional circumstances.
The study does not include drinking water standards.
The report comes as the Government finalises a plan on river basin management which will protect such waters for the next four years.