The new EU nitrates regulations, putting in place the controversial plan for the protection of ground-water from agricultural pollution, came into force yesterday.
The most contentious of the regulations, however, limiting the use of fertilisers on land, will not become law until January 1st.
That will limit the amounts of nitrogen and phosphorus fertiliser farmers will be allowed to spread on their land and will also limit the areas and the times of year it can be spread.
The farm organisations have opposed the limit of 170kg a hectare a year of organic nitrogen, saying it will drive Ireland's most progressive farmers out of business as they will not be able to farm commercially within the law.
The sector has received a commitment from the Government that it will seek a derogation from the EU to allow them to spread up to 250kg a hectare a year. That process is well under way.
Ireland had been resisting the introduction of fertiliser limits for well over a decade but was eventually forced to concede to Europe under pain of daily fines from the European courts.
The campaign saw the farm bodies pull out of the national partnership talks for some time and political observers say it will continue to be a political issue at the next general election.
The regulations are to be implemented over a five-year period and will involve substantial investment in manure storage facilities.
Special provisions have been negotiated for the management of manure from the pig, poultry and mushroom sectors and grants have been made available for new disposal systems. Funding is available for investment in emerging technologies, including aerobic/anaerobic digestion systems and fluidised bed combustion, and to support appropriate agri-environment research projects
Minister for Agriculture Mary Coughlan promised recently the circulation of the nitrates guidance document to all farmers would be accompanied by a series of information meetings in early autumn.