Water in hundreds of rivers, lakes, estuaries, groundwater bodies and along our coasts is failing to reach acceptable quality standards.
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 cause excessive growth of water based plants.
On the agricultural side, the problem comes from nutrients such as 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 most pollution are the south and southeast, 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.
Irish Water has issued a statement following the report, recognising the role that wastewater discharges has on water quality.
The organisation says the report is a timely reminder of the decades of under investment in wastewater infrastructure in Ireland and the lack of standardised operation and maintenance provided by the industry, which was fragmented and under-funded up to 2014 when Irish Water was established.
This has had an impact on communities all around the country.
Irish Water has a plan to address the issues and concerns, raised by the EPA, and is already making progress.
The report comes as the Government finalises a plan on river basin management which will protect such waters for the next four years.
Andy Fanning, the EPA's Programme Manager, has said untreated sewage getting into Irish waters continues to be a problem.
He said the EPA's latest report has identified 43 locations where there is no treatment for sewage and it continues to get into Irish waters.
Speaking on RTÉ’s Morning Ireland, he said the EPA has been very vocal in relation to untreated sewage being discharged into estuaries.
He said: "It is not acceptable. The EPA is calling for sustained and increased funding for Irish Water to address these problems."
He said agriculture, forestry and other land practices are other key impactors.
In a statement, the Department of Planning, Housing and Local Government said that it notes the report by the EPA and the challenges facing Ireland in improving water quality.
The department says that last February the Minister for Planning, Housing and Local Government published a draft river basin management plan for 2018-2021, "which outlines proposed measures aimed at protecting and improving the water environment".
It says that there has been six months of public consultation on the draft plan, which ends today.
The department says that a plan will then be finalised and the minister will publish the final plan in the coming months,