Local authorities inspected 4,315 farms last year under the Good Agricultural Practice (GAP) for Protection of Waters Regulations.
This represents a 66% increase on 2024 and is 96% of the annual target of 4,500 inspections set by the Environmental Protection Agency (EPA).
The inspection targets prioritise areas where agricultural activity poses the greatest risk to water quality.
22 of the 28 local authorities that carry out farm inspections have met their 2025 targets, compared with only 8 local authorities in 2024.
Cork County Council again recorded the highest level of farm inspections at 1,244, followed by Tipperary (496), Meath (488), and Wexford (433).
The EPA's National Agricultural Inspection Programme (NAIP) report shows that of the 4,315 farms inspected by local authorities in 2025, 43% were found to be non-compliant.
The top three reasons for non‑compliance were: poor control of soiled water; discharges with potential to impact water quality and inadequate management of farmyard manure.
The number of follow-up GAP inspections doubled to 1,280 compared with the previous year.
48% of farms had remediated the issues and achieved compliance after these inspections.
The EPA said that "poor farming management practices can pollute rivers, streams and coastal waters through the release of nutrients, such as nitrogen and phosphorous".
The agency added that harmful pathogens and nitrates may also pose a risk to human health through contamination of drinking water sources.
The EPA said that 2,935 enforcement actions were taken by local authorities in 2025, 68% higher than the previous year.
However, the report noted that "prosecutions and cross‑reporting remained low".
199 farms were cross‑reported to the Department of Agriculture, Food and the Marine (DAFM) for non‑compliance, resulting in Basic Income Support for Sustainability (BISS) payment penalties.
DAFM carried out 631 inspections on behalf of local authorities with 129 farms received penalties ranging from 1% to 40% of their BISS payments.
One farm that refused inspection received a 100% penalty on their BISS payments.
The report also shows that an additional 1,555 non‑GAP farm inspections were conducted by local authorities in 2025, arising from planning applications, environmental incidents and public complaints.
Dr Tom Ryan, director of the EPA’s Office of Environmental Enforcement, welcomed the significant increase in the number of farm inspections carried out by local authorities in 2025.
"Agriculture remains a significant pressure on our water quality and the non-compliance rate found during inspections remains too high.
"Farm compliance with the Good Agricultural Practice for Protection of Waters Regulations is essential to protecting and improving water quality.
"In addition, a more consistent and sustained enforcement effort is needed across all local authorities to ensure full compliance with these regulations and to protect public health and the environment," he said.
Ray Cullinane, acting programme manager at the EPA's Office of Environmental Enforcement added that "local authorities must sustain the increased level of farm-inspection activity achieved in 2025".
"To address the high non-compliance rate, local authorities should increase follow-up inspections to close out outstanding cases and ensure full compliance with the relevant Regulations.
"In parallel, local authorities, advisory services and industry stakeholders must also strengthen compliance-promotion and awareness-raising activities to support farmers in meeting their regulatory obligations," he said.
An enhanced compliance and enforcement scheme formed part of Ireland's fifth Nitrates Action Programme (NAP).
As part of this, an expanded enforcement role was assigned to the EPA in relation to oversight of local authority farm inspections.