The Environmental Protection Agency (EPA) has called for a reduction in nitrogen fertiliser usage by farmers to halt a significant decline in water quality.
The EPA report says a third of rivers and lakes and a quarter of estuaries are failing to meet their nutrient-based environmental quality standards.
Over a quarter of monitored river sites are now seeing increasing phosphorus and nitrogen concentrations.
There are now just 20 pristine river sites, the report found - down from over 500 in the late 1980s.
The EPA says excess nitrogen impacts is a concern, particularly in the south and southeast of the country, where losses to the marine environment are elevated and increasing.
"In these areas, the soils are relatively freely draining and are very susceptible to nitrogen leaching from agriculture, which is often intensive," stated the Water Quality in Ireland report for 2018-19.
"In these areas nitrate losses are closely correlated with farm intensity; the higher the application of nitrogen to land, the higher the nitrate concentrations in waters.
"Since 2013 nitrogen emissions have increased as both cattle numbers and fertiliser use have increased. Nitrogen loss reduction measures need to be targeted in these areas by improving nutrient use efficiencies and by reducing chemical fertiliser use."
Mary Gurrie, the EPA's water programme manager, said: 'The overall increase in nutrient concentrations is a worrying development for our water quality.
"These excess nutrients come from human activities, predominantly our farms and waste water.
"We need to address the sources and the pathways by which these nutrients make their way into our rivers and lakes."
Meanwhile, the national federation for group water schemes has proposed that farmers in some areas be paid to farm less intensively.
The EPA's report found that only 50pc of lakes were in good health, although that was an improvement on previous years, while just 38pc of estuaries were in good health which was down from the previous assessment.
The amount of phosphorous found in the estuaries jumped by a third from 2013, while nitrogen concentrations were up by 16pc.
The report describes the loss of high status waters as "one of the most worrying trends".
"These near pristine unpolluted water are vital for the survival of sensitive aquatic species and the protection of aquatic biodiversity," it stated.
It said that the numbers have fallen by a third since 2009 alone.
Coastal waters fared better with 80pc in good health, along with 87pc of canals and 92pc of groundwater.
Responding to the report IFA President Joe Healy said it’s high time that local authorities and Irish Water addressed the illegal pumping of raw sewage into our rivers and streams.
“Ireland stands guilty before the ECJ of one water quality issue and that’s non-compliance with the Urban Waste Water Treatment Directive, which was introduced almost 20 years ago. This has led to raw sewage with high phosphorous and nitrogen concentrations from the equivalent of 77,000 people being released into our waters every day”.
Regarding farming’s contribution to a better rural environment IFA President Healy said, “Over the past decade, farmers have spent over €2.5bn bringing their farmyards up to the highest environmental standards.
"Also, over 40pc of all farmers in Ireland take part in the Department of Agriculture’s Green Low Carbon Agri-Environment Scheme (GLAS), which is over-subscribed and closed to new entrants," he said.
In addition, Healy said the introduction of the following measures will lead to better water quality in rural areas: