The European Commission is threatening to take the country to court over eight cases that could result in fines of tens of thousands of euro a day.
Ireland has one of the worst environmental records in the EU, receiving twice as many first warnings last year as France, which has ten times the population.
The commission issued a first warning over the government's failure to properly tackle the problem of farming nitrates running into the groundwater.
The European Court found Ireland guilty of failing to produce a plan to reduce the nitrates risk. Last year they produced one, but the limits it stipulated are far too low to be effective.
The commission said the original plan about which the public was consulted in December 2003 was acceptable, but they seriously weakened the final version.
Environment Commissioner Stavrosby Dimas said: "The programme needs serious strengthening in key areas if it is to contribute successfully to securing clean water for Irish citizens."
Dublin MEP Proinsias de Rossa was very critical of the Government's record: "The commission's announcement is a terrible indictment of this Government's environmental record."
The Government could find itself in front of the court again within three months and if found guilty could be fined thousands of euro a day until they have rectified the problem.
The commission issued final warnings about seven other breaches of environmental laws.
The need to upgrade waste-water treatment plants in six towns Sligo, Bray, Shanganagh, Howth, Letterkenny and Tramore.
Failure to stop smells from water and sewage treatment plants, including the new 300m plant in Ringsend, Dublin.
Not regulating the dumping of dangerous waste including arsenic and lead from the Tynagh mines in Co Galway.
Threatening the wild birds' habitat in the Boyne estuary by failing to remove waste left from dredging.
Damaging the ozone layer by not replacing ozone depleting substances in various goods including pesticides for crops and fire fighting equipment.
Not having a plan to reduce air pollution by poisonous substances including sulphur dioxide.
Not carrying out an environmental impact assessment on the country's largest wind-farm project in Derrybrien, Co Galway, before or since the massive landslide in October 2003.
Mr de Rossa said Ireland has one of the worst records when it comes to respecting European environmental laws.
"In the five years to 2002, the commission issued more first warnings over environmental breaches by Ireland than against the Netherlands, Austria, Sweden, Finland, Luxembourg and Denmark combined 85 versus 77," he said.