The Avoca river in Co Wicklow was found to be the State's most contaminated river when analysed for heavy metals.
The report noted however that the finding was not a surprise as the presence of metal is attributable to the now defunct copper mines.
While the quality of water was recorded as good "but under pressure" in the Royal and Grand canals, the quality in the Shannon River basin continued to deteriorate, according to the EPA.
An increase in slight and moderate pollution was recorded broadly but serious pollution was recorded in nine rivers in the period under review. These were the Lee (Tralee) in 2001; the Brosna below Mullingar; the Tullamore below the town; the Jiggy (Hind) below Roscommon; the Rhine below Granard; the Ahavarraga below Drumcolliher, Co Limerick; the lower Broadford and the Loobagh below Kilmallock, Co Limerick, all in 2002; and the Graney below Scarriff in 2003.
Most of the lakes classed as severely eutrophic - or hypertrophic - were in the north midlands area. Of the State's seven river basin districts, the western had the highest proportion of lakes of a satisfactory standard.
The study also found acid run-off from afforestation in a feeder stream to the Glendalough lakes in Co Wicklow. However, other acid-sensitive lakes in Galway and Donegal, Maumwee and Veagh, respectively were found to be unimpaired by forestry.
Some 12 estuaries and coastal waters out of a total of 69 assessed were found to be eutrophic. Three more were assessed as potentially eutrophic, 28 of intermediate status, and 26 as unpolluted. The eutrophic waters include parts of the Broadmeadow in Co Dublin; the Slaney in Co Wexford; and the Blackwater and Bandon in Cos Waterford and Cork respectively.
Monitoring of the quality of 122 bathing places found 97 per cent of the sites were in compliance with mandatory standards set by the EU Bathing Waters Directive.
There were 10 instances of non-compliance in the three-year period but no site failed in more than one of the three years. Some 60 per cent of the designated beaches were awarded Blue Flag status during the period.
