Key Contact: Alice Whittaker – Chairperson and Partner |
Underlying all of these problems of introducing contamination into our world is the question of moral responsibility — responsibility not only to our own generation but to those of the future. – Rachel Carson
According to the 2025 EPA Report on Water Quality in Ireland, 44% of river sites, mostly in the south and southeast of the country, have high nitrate concentrations while over a quarter of river sites (27%) and a third of lakes (32%) have elevated phosphorus concentrations. Transitional and coastal water bodies are the ultimate receptors of the excess nutrients in our rivers and lakes. The amounts of nitrogen and phosphorus flowing into our estuaries have been too high in recent decades and the ecology of our estuaries, particularly in the south and southeast has declined precipitously as a result. Transitional water bodies are in the poorest condition of any water body type with 70% in unsatisfactory condition which is a 5% decline on the previous assessment. Many of these coasts and estuaries are important areas for marine life and for birds, designated for their protection under the EU Habitats and Birds Directives.
According to the EPA Report, the three biggest culprits for poor and deteriorating surface water quality are:
- Agricultural run-off;
- Physical interference with water courses; and
- Inadequate or lack of wastewater treatment.
Of these three, agricultural run-off is the primary culprit and arguably the easiest to address, yet successive Governments have continued to seek a derogation from the limits set under the Nitrates Directive.
Meanwhile, water quality in our lakes, rivers and estuaries, particularly in certain parts of the country, have continued to decline. While this is disastrous for the environment and for human health and well-being, it is also disastrous for Ireland’s economic and social ambition to have adequate housing and infrastructure provision.
Delivery of critical and cost-efficient infrastructure such as flood relief schemes and wastewater treatment systems is made all the more difficult because the underlying baseline water quality status is poor and/or deteriorating, and because natural habitats and the habitats of species are being allowed to degrade and deteriorate.
All of this is contrary to EU law.
For example, Article 4 of the Water Framework Directive (WFD) requires Ireland to:
- Protect, enhance and restore water quality, and
- Adopt measures to prevent deterioration of water quality.
The EPA Water Quality Report indicates that Ireland is failing with both of these obligations.
Articles 6(2) and (3) of the Habitats Directive provide that Ireland shall:
- Take appropriate steps to avoid the deterioration of Natura 2000 sites and the significant disturbance of the species for which those sites are designated, and
- Ensure that an Appropriate Assessment (AA) of the implications for a Natura 2000 site is carried out before consent is given for a plan or project likely to have a significant effect on the site, and only consent to such plan or project after having ascertained that it would not adversely affect the integrity of the Natura 2000 site.
The 2025 Status of EU Protected Habitats and Species in Ireland report published by the National Parks and Wildlife Service indicates that Ireland is also failing with these obligations.
Bodies like An Coimisiún Pleanála, the EPA and County Councils must not authorise or allow a plan or project if it would contribute to (i.e. fail to prevent) the deterioration of water quality, or if it would have adverse effects on the integrity of a Natura 2000 site. These are strict legal tests, enforceable through the judicial review of planning, licensing and other decisions of public authorities.
The degraded state of our natural environment, particularly water and habitats, makes the delivery of infrastructure and housing all the more difficult.
While the finger of blame points towards the the innocent freshwater pearl mussel, or the committed E-NGO, the root cause of the difficulty – the legacy of successive failure to prevent water pollution and habitat degradation – is largely ignored.
Meanwhile, local frustrations grow because Uisce Eireann and the Office of Public Works are struggling to secure the necessary consents to deliver cost-effective and efficient wastewater treatment and flood relief infrastructure against a baseline of poor and deteriorating water quality and habitats.
Agricultural run-off and the Nitrates Derogation
Under the Nitrates Directive 1991/676/EEC, each Member State was to impose maximum limits in livestock manure nitrogen concentrations of 170 kg N/ha, however since at least 2007 Ireland has availed of a derogation, authorised by the European Commission by a succession of decisions (2011/127, 2014/112, 2018/209, and 2022/696), whereby certain farms with at least 80% grassland are permitted to apply livestock manure nitrogen up to 250 kg N/ha, subject to conditions and controls prescribed by the relevant Nitrates Action Programme (NAP) and EC (Good Agricultural Practice) Regulations S.I. No. 113/2022 as amended by S.I. No. 42/ 2025(GAP Regulations).
Ireland’s fifth NAP was adopted in 2022 and was due to expire by the end of 2025. Pursuant to the NAP and GAP Regulations, the Department of Agriculture, Food and the Marine (DAFM) would grant annual derogations to individual qualifying grassland farms permitting livestock manure nitrogen concentrations of up to 250 kg N/ha, subject to conditions (Farm-level Derogations).
Ireland is the last EU Member State to seek derogations from the Nitrates Directive. The Dutch Government ceased granting derogations following the ruling of the CJEU in the “Dutch Nitrates” Cases C‑293/17 and C‑294/17, which found that the activity of applying fertilisers on farmland and grazing cattle, where such activities are likely to have a significant effect on a Natura 2000 site, can be a “project” for the purposes of Article 6(3) of the Habitats Directive, and that an Appropriate Assessment (AA) should be carried out prior to granting an Individual Farm-level Derogation, unless it can be established that an AA at the level of the NAP is capable of satisfying the requirements of Article 6(3) of the Habitats Directive. The Dutch national court subsequently determined that the AA of the Dutch nitrates action plan left an “assessment gap”, and ultimately the Dutch Government abandoned its derogation regime.
Ireland does not carry out AA prior to granting individual Farm-level Derogations, and relies instead on the AA and Strategic Environmental Assessment (SEA) undertaken prior to making the fifth NAP and the subsequent revisions and modifications thereto made in 2025.
Critically, when authorizing Ireland’s fifth NAP in 2022, the European Commission attached two requirements. First, Ireland was required to review water quality implications of the derogation regime on surface waters and to reduce the ceiling from 250 to 220 kg N/ha in areas with higher nitrates concentrations and/or worsening eutrophication trends. Second, Ireland was required to demonstrate that it complied with the requirements of Article 6(3) of the Habitats Directive in carrying out an AA of the proposed NAP, per the Dutch Nitrates case. The review of water quality undertaken jointly by DAFM and the EPA revealed that a reduction in nitrates applications to the lower derogation level of 220 kg N/ha would be required across a significant number of derogation farms and additional control measures were applied by S.I. No. 42/ 2025.
Ireland then persuaded the European Commission to have the authorisation of the derogation extended to 2028. The Commission Decision C(2025) 9263 was confirmed on 22 December 2025, pursuant to which Ireland is required to:
- Complete assessments of the Farm-level Derogations on Ireland’s European sites pursuant to Article 6(2) and Article 6(3) of the Habitats Directive, and Article 4(1) of the Water Framework Directive by the end of 2028;
- Review the NAP and GAP Regulations, taking into account the results of those assessments;
- Require the transportation and re-distribution of slurry away from already overloaded farms, or apply a lower chemical-nitrates allowance on those farms;
- Increase manure and soiled‑water storage capacity on farms by 1 October 2028,
- Lower the crude‑protein cap to 14% for dairy and older cattle at grass; and
- Further reduce maximum chemical‑nitrates allowances and widen fertilizer buffer zones in catchments with persistent water quality issues.
RENURE – Amendment to the Nitrates Directive and Biomethane Strategy
In February 2026, an amendment to the Nitrates Directive was approved which, when implemented, will allow Ireland to authorise the application of processed manure fertilisers, such as digestate from Anaerobic Digestion (AD) to be applied above the 170 kg N/ha limit, subject to compliance with specifications and parameters to ensure no adverse impact on water quality or the environment. Farm manures diverted to AD plants and combined with other farm wastes and grass stock may be used in the production of biogas and ultimately biomethane for injection to the natural gas grid and/or other purposes. The AD digestate may then eligible for use as “RENURE” fertilisers on suitable agricultural land.
The Irish Government has committed in the National Biomethane Strategy to a target of up to 5.7 TWh per annum of locally produced biomethane by 2030, and the Commission for Regulation of Utilities has approved Gas Networks Ireland’s interim solution for reverse grid compression, removing a material infrastructure constraint that limits biomethane injection capacity across Ireland’s regional networks. These are among the measures designed to accelerate Ireland’s progress toward the national biomethane target while a permanent regulatory framework is developed.
It remains to be seen whether legacy water quality issues will hamper implementation of Ireland’s Biomethane Strategy and “RENURE” as planned, and whether the environmental specifications and controls will be sufficient to avoid further deterioration in water quality and degradation of habitats. One of the difficulties is the transport and logistics costs associated with moving farm manures and other materials to AD plants and moving digestate “RENURE” to the farmlands eligible to apply it.
Current challenge to Ireland’s Nitrates Derogation Regime
In two separate and connected references from the Irish High Court to the CJEU – Case C‑531/24 (An Taisce I) and Case C‑895/24 (An Taisce II) – the CJEU is asked (in summary):
- Whether it is consistent with the SEA and Habitats Directives for the SEA and AA of the fifth NAP to limit their assessments to the protective measures in the NAP and GAP Regulations (Plan-level SEA/AA), or whether it was instead necessary to carry out an AA and SEA of the specific effects of agricultural activities under the Individual Farm-level Derogations that would be granted pursuant to the NAP, once adopted (Farm-level SEA/AA).
- Whether it was necessary under Article 4 of the WFD to ensure, by way of objective scientific evidence, that the implementation of the fifth NAP including Derogation Regime would not result in the State’s failure to: (a) protect, enhance and restore water quality, and/or (b) prevent deterioration of water quality.
- Whether it was necessary under the SEA Directive to: (a) assess the environmental effects of alternatives to the fifth NAP and Derogation Regime in a comparable way to the SEA of the NAP; or (b) limit the assessment of effects of the NAP on “material assets” by reference to its environmental effects on such assets, and to not give undue weighting to broader socio‑economic concerns, such as adverse effects on farm income and sectoral sustainability.
- Whether, if the fifth NAP was found to have been adopted in breach of the Habitats Directive, WFD or SEA Directive, this would have the effect of invalidating the Commission’s Implementing Decision (2022) approving the NAP and associated Derogation Regime.
Following a hearing in December at which submissions were made by An Taisce, the Irish Farmers Association, the Irish Creameries and Milk Suppliers Association, the Irish Government and the European Commission, Advocate General Kokott delivered her Opinion to the CJEU on 26 March 2026.
A final ruling of the CJEU is awaited and it remains unclear whether the CJEU will follow the AG’s Opinion or rule otherwise.
Habitats Directive
In the (admitted) absence of an Individual Farm-level Derogation AA procedure, the Opinion finds that the onus is on Ireland to demonstrate that it has undertaken a Plan-level AA that is sufficient to meet the requirements of Article 6(2) and 6(3) of the Habitats Directive. The AA that was undertaken prior to the adoption of the Fifth NAP in 2022 did not establish that, together with the Derogation Regime, it would ensure no adverse effects on the integrity of European sites from increased nitrogen application. AG Kokott noted Ireland’s intention (as communicated to the European Commission in late 2025) that compliance with the Habitats Directive would be achieved in the future with catchment-based AA, however she noted that future intentions do not satisfy current compliance requirements. The Opinion concludes therefore that the AA of the Fifth NAP lacked the necessary complete, precise and definitive conclusions capable of removing all reasonable scientific doubt as to the absence of adverse effects on European sites.
Water Framework Directive
The Opinion concludes that the adoption of the fifth NAP lacked the necessary assessment and conclusion required by Article 4 of the WFD that the measures in the NAP and GAP Regulations would adequately protect, enhance and restore good environmental status to the relevant surface water bodies, and would prevent deterioration of such water quality. Having regard to the relevant EPA and DAFM monitoring results, it was clear that the Derogation Regime was not having that effect. Ireland had also failed to establish that the circumstances for a derogation from the WFD requirements are applicable in this instance. The Opinion concludes that the adoption of the NAP in the absence of a full and comprehensive WFD assessment was in breach of Article 4 of the WFD.
SEA Directive
The Opinion concludes that the SEA of the fifth NAP required an assessment of reasonable alternatives, and whilst this does not mean that a full SEA is required for each such alternative, the details and assessment of alternatives to the plan must be sufficient to show how environmental effects were taken into account in selecting the preferred plan. The Opinion further concludes that when assessing “material assets” in an SEA, the focus is the environmental effects of the proposed plan on material assets, not a broad assessment of the socio-economic benefits or impacts of the plan on farm income, employment etc.
The Opinion concludes, therefore, that an SEA must assess alternatives in sufficient detail to enable a person to understand how environmental effects were taken into account and it is not sufficient to engage in a cursory discussion entirely lacking in comparative detail. Broad socio-economic factors cannot be relied upon to outweigh or dismiss environmental effects.
Validity of Commission’s Implementing Decision
The Opinion does not directly address this issue, determining that it would be premature pending the national Court’s ruling on whether the NAP and corresponding AA / SEA are in breach of the relevant Directives, a finding that the Opinion does not go so far as to make. The Opinion points out, however, that whereas the CJEU has in the past decided that a measure may be suspended or repealed pending compliance, compliance in this instance might not be possible or practically achievable.
The Opinion confirms that the Commission’s authorisation of derogations in the past does not relieve Ireland of the binding obligations imposed by EU law, and notes that the Commission’s decisions were made expressly without prejudice to Ireland’s obligations as interpreted by the CJEU – in Dutch Nitrates and An Taisce I and II.
The CJEU’s final ruling in the matter will be keenly awaited.
Accelerated Infrastructure and Housing – Constraints on connecting new projects
Meanwhile Uisce Eireann is being given more funding and budgetary certainty, flexibility and power to focus on delivering priority projects pursuant to the actions committed to by Government under the Accelerating Infrastructure Report and Action Plan published in November 2025. It is recognised that unless sites are connected with water/wastewater and power, housing cannot be delivered at the scale required to meet current and future demand.
As many areas of the South and South East flooded this Winter and Spring, the OPW is being called upon to accelerate flood relief works despite various planning challenges and set-backs along the way.
The challenge is delivery against a baseline and legacy of poor and deteriorating water quality and habitats that are degrading due to legacy pollution and run-off. The relevant consenting authorities are being asked to establish, prior to granting consent, that the proposed project will not have adverse effects on the integrity of a Natura 2000 site, the integrity of which is already undermined through years of neglect and abuse. At the same time, the consenting authority is being asked to conclude that the proposed project will not result in the deterioration of water quality – even temporarily – against a baseline of water quality that is already deteriorating.
The alternative approach is to rely in the consenting process on derogations available under Article 6(4) of the Habitats Directive or Article 4(6) and (7) of the WFD, however these are restrictive procedures, to be availed of in exceptional circumstances and in the absence of alternatives. This slows things down and increases costs and complexity exponentially – particularly if the same scenario is repeated across multiple projects and sites across Ireland.
Instead of pointing at the glorious freshwater pearl mussel or blaming E-NGOs for bringing these issues to the attention of the Courts, it is necessary to break through siloed thinking and view environmental protection, enhancement and restoration, as central to Ireland’s economic and social objectives.
