Ireland faces a "major policy challenge" to implement the EU Water Framework Directive because of persistent pollution of rivers and lakes as well as groundwater and even drinking-water supplies.
The recently-adopted directive provides for a more integrated approach to controlling water pollution and "should ultimately lead to significantly improved water quality and water management across the State", according to the EPA.
In its report on the current state of the environment here, the agency points to intensive agriculture as the principal culprit for water pollution, primarily because of the still-excessive use by farmers of phosphate and nitrate-based fertilisers.
It says Ireland's game fish population is threatened by the eutrophication (over-enrichment) of surface waters by phosphorous and nitrates, describing this as "one of the most serious environmental pollution problems" we face.
An assessment carried out last year found that 13 bays or estuaries were eutrophic and four others were considered to be potentially eutrophic.
In response, 30 new water bodies were designated as "sensitive areas" to nutrients.
Though the most recent assessment of river water quality showed an improvement in water quality for the first time since surveys began, the EPA concedes that over 30 per cent of river channel is "still considered to be polluted to some extent".
While the number of fish kills had fallen from a high of 112 in 1987 to 25 last year, there had been upsurges in 1995 and 2000 due to discharges of silage liquors, animal slurries and sewage.
To minimise water pollution from agricultural sources, it says, there is a need to promote better farmyard management, reduce the over-application of fertilisers and implement nutrient management planning on a broad river catchment basis.
Referring to groundwater quality, it notes that many areas "show an unacceptably high level of bacteriological contamination", with supplies in counties Carlow, Cork, Kerry, Louth and Waterford identified as being polluted by agricultural nitrates.
The report points out that groundwater accounts for about a quarter of the total water abstracted for drinking water supplies and as much as 85 per cent in rural areas. Altogether, it estimates that there are at least 200,000 wells throughout the State.
In the period 1998-2000, it was found that 38 per cent of samples tested were contaminated by bacteriological pollution from such sources as septic tank effluent, agricultural waste and landfills. This was an increase of 4 per cent over 1995-1997.
"The maximum admissible concentration for total coliforms in drinking water is zero. The latest report on drinking water quality in Ireland shows that 91 per cent of public supplies and only 58 per cent of group schemes meet that standard."
In most cases, group water supplies had been contaminated by "improperly sited septic tanks and slurry pits, direct animal access to water sources, intensification of animal-rearing and inappropriate land spreading of animal manures".
Though €533 million had been pledged to upgrade rural water schemes from 2000 to 2006 and some pilot treatment programmes were "bearing fruit", there was also a need for better management of farm wastes and disinfection of private supplies.