About 52km of Ireland's rivers are seriously polluted, the lowest level in decades.
A study by the Environmental Protection Agency (EPA) has found just 20 rivers were severely affected - half of what it was five years ago - between 2007 and 2009.
Twenty-five lakes were assessed as poor or bad, with 15 of them in Cavan and Monaghan.
The extensive water quality report also looked at tidal areas and found eight areas in a poor state mainly due to waste treatment plants, and it warned that bathing areas Balbriggan in Dublin and Clifden in Galway were consistently the worst.
Micheal O Cinneide, director of the EPA office of environmental assessment, said Ireland is above average in EU terms.
"While there is evidence of an overall improvement in water quality in Ireland, further actions are essential if we are to achieve our water quality targets for 2015 and 2021 as required by the Water Framework Directive," he said.
Martin McGarrigle, from the EPA's aquatic environment monitoring team, said: "The three challenges for water quality management are firstly, eliminating serious pollution associated with point sources, that is wastewater treatment plants; secondly, tackling diffuse pollution, meaning pollution from farming and septic tanks; and thirdly, using the full range of legislative measures in an integrated way to achieve better water quality."
Experts checked 1,700 rivers running to 13,118km, 222 lakes, 89 estuaries and coasts and 211 areas of groundwater.
Three bathing areas on lakes failed to meet EU cleanliness standards while around the coasts eight areas were named for not reaching sufficient standards - Balbriggan front strand, Skerries south beach, Sutton burrow in Dublin, Clifden, Dunmore Strand in Waterford, Duncannon in Wexford, Killala Ross in Mayo and Youghal in Cork.
The extensive study found, in total, a third of the river course contains some pollution - eight because of wastewater treatment plants and the rest because of farming practices.