Environmental groups have criticised the National Farmers Union for helping hundreds of agricultural businesses to push back against measures designed by the Department for Environment, Food and Rural Affairs to protect vulnerable rivers in the UK.

Working with the specialist consultancy Hafren Water, the NFU has helped at least 200 land users in nearly 40 river basins and groundwater catchments to fight against “nitrate vulnerable zone” designations, according to documents made available to the union’s members.

Farmers operating in areas of the UK that are designated as nitrate vulnerable zones are required to comply with restrictions related to the use of fertilisers and the storage of organic manure, designed to reduce the risk of pollution leaching into waterways.

In a video made available to union members, the NFU announced that its legal board had agreed to make special financial support available to agricultural businesses that wanted to appeal against these designations through its legal assistance scheme.

In the video, which was obtained by the investigative journalism organisation Point Source, an in-house solicitor for the NFU said the organisation’s legal assistance scheme would fund the entire cost of preliminary research and consultations before the formal appeals process.

The solicitor also said the scheme would provide subscribers with financial contributions towards costs during the formal appeal proceedings.

The NFU encouraged members to form groups to share costs and work with Hafren Water to challenge designations, saying the consultancy could be trusted and had previously “fought really hard on behalf of members”.

In a document accompanying the video, the NFU said it had “enjoyed a good degree of success” working on nitrate vulnerable zone appeals with Hafren Water in the past.

The NFU declined to tell the Guardian how much money it had already provided to support appeals against designations.

Under the existing system farmers are given an opportunity to appeal against designations every four years.

During the last round of appeals, which started in 2017, 94 of 135 were successful.
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The appeals that the NFU and Hafren Water helped farmers to win included removing designations from the River Calder in Lancashire and the River Dove in the Midlands. Together their catchments cover an area of about 1,500 sq km (580 sq miles).

No English rivers have good chemical status and only 14% have good ecological status, according to the most recent Environment Agency figures published under obligations originally established by the EU water framework directive.

Environmental organisations were highly critical of the NFU’s efforts to push back against designations intended to reduce pollution in waterways.

Runoff from agriculture is the biggest single polluter of English rivers, responsible for 40% of damage to waterways.

The chief executive of Salmon & Trout Conservation, Nick Measham, said: “The NFU’s efforts to reduce the number of designated nitrate vulnerable zones in the UK is part of a broader push to deregulate farming.

“The organisation is pushing to remove designations even if it is clear that their removal will result in worsening ecological conditions for already degraded waterways.

“What the NFU should be doing is using its resources to make members true stewards of the countryside instead of seeking to game regulations so that farmers can increase their profits at the expense of the environment.”

The head of science and policy at the Rivers Trust, Rob Collins, said: “Nitrate vulnerable zones are designed to prevent excessive levels of nitrate from polluting surface and groundwaters, causing eutrophication and requiring costly water treatment.

“Rather than challenging designations, funds would be better spent supporting farmers to optimise fertiliser application through nutrient management plans and improving slurry management.”

During the latest round of appeals the Environment Agency has received 55 applications across nine river basin districts, according to information obtained by Point Source using freedom of information legislation.

Defra said Hafren Water was named as the representative acting on behalf of owners or occupiers for 14 appeals.

None of the appeals have been heard yet in the current round, which is the first since Britain left the EU.

David Baldock, a senior fellow at the Brussels-based Institute for European Environmental Policy, said organisations that opposed restrictions on fertiliser use could achieve significant change during the forthcoming appeal hearings.

“The NFU has always had its sights set on trying to push back against these nitrate regulations,” he said. “Previously Defra was under pressure from the European Commission to report back and demonstrate that they were complying with the EU nitrate directive, but now that Britain has left the EU this is no longer necessary.

“Defra’s reaction to these appeals is going to be one of the tests of its resolve to maintain standards of environmental legislation after Brexit.”

Nitrate vulnerable zones covered about 69% of England in 2009. Over the past decade, this figure has been eroded and during the last round of appeals it was reduced from about 58% to 55% of the country.

In a statement the NFU said: “Farmers are perfectly entitled to follow that appeals process to ensure that the designation is correct and has been applied fairly. NFU members are able to seek guidance and support from our legal assistance scheme to help with the appeals process.”

Hafren Water said: “The decision as to whether an area should be designated as a nitrate vulnerable zone is entirely objective and determined using catchment-specific data and Defra-derived methodology.”

A Defra spokesperson said: “We are committed to working with farmers to improve water quality through advice, incentives and effective regulation. Our goal in the agricultural transition plan is for a modern approach where farmers and regulators work together to improve standards, underpinned by credible deterrents for severe or serial harm.”