WWF-UK, the Angling Trust and Fish Legal have joined forces to launch a legal challenge after accusing Defra and the Environment Agency of failing to protect our 'most precious rivers' from agricultural pollution.

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The conservation campaigners say they have been granted permission by the High Court for a judicial review, arguing that the government is failing in its legal duties, set out under the EU Water Framework Directive (WFD).

Their case focuses on areas known as Natura 2000 sites, including several East Anglian habitats where the groups blame poor land management for causing soils carrying nutrients and pesticides to wash into the waterways, harming fish and other wildlife.

Although the region's farming leaders argue that significant progress has already been made to minimise diffuse pollution, the campaigners say the government has failed to take the 'necessary steps' to meet their target of ensuring protected rivers are in good health by December 2015.

Mark Lloyd, chief executive for the Angling Trust and Fish Legal, said: 'This pollution is not only bad for fish and wildlife, but also anglers who contribute billions to the economy every year. We must ensure the necessary measures are in place to stop this pollution, and give our rivers and lakes a chance to recover and thrive.'

The National Farmers' Union (NFU) said 35pc less nitrogen fertiliser and 60pc less phosphate fertiliser are being applied to the fields now compared to peak levels in the 1980s.

Rob Wise, the NFU's environment advisor for East Anglia, said a supportive partnership between landowners, legislators, and conservation groups was the best way to finding a long-term solution.

'We are actually sitting locally with these conservation groups in the Anglian river basin management panel, and in individual catchment partnerships which are working together on solutions for rivers in many of these areas.

'So it is disappointing that they feel the need to elevate this to the courts on the premise that the EA is failing on its commitments to improve the health of these rivers by 2015. Quite clearly, that is an aspiration of the WFD, but the directive acknowledges it may take more years than that to do it. It has fallback dates of 2021 and 2027 by which these very complex standards need to be met.

'So it seems entirely premature and somewhat provocative to suggest everybody is failing at this, given that these rivers are improving.

'To launch an attack on the government at a time when government has just finished consulting on a river basin management plan for the next six years seems to be unnecessarily upsetting the apple cart.'

A Defra spokesman said: 'Rivers in England are the healthiest they have been for 20 years and we are committed to working closely with the farming community and environmental groups to further improve water quality.

'Over the next five years, we are investing more than ever to promote environmentally-friendly farming practices to protect our rivers and lakes and support wildlife. We are unable to comment on any ongoing legal proceedings.'

The Norfolk Rivers Trust was established in 2011 with the objective of conserving and restoring the county's rivers and wetland habitats.

Project officer Helen Mandley said: 'There are so many different sources of sediment getting into a river. Agriculture is one of them – it is going in the right direction, but it is still a problem in places.

'As well as sediment there is the nutrient side of things, with phosphate and nitrate fertilisers getting washed off fields during heavy rainfalls and into our rivers and ditches. We want to do more monitoring as we need to have more evidence to help our fight against sediment getting into rivers, but funding is hard to come by.'

Protected species

The 50 protected sites listed by the campaigners include Special Protected Areas (SPAs) and Special Areas of Conservation (SAC) which are home to important and legally-protected wildlife.

Among them is the River Wensum, also designated as a Site of Special Scientific Interest (SSSI) which is an essential habitat for species such as water voles, white-clawed crayfish, kingfisher, brown trout, eels and otters.

The Broads are Britain's largest protected wetland and are home to some of Norfolk's rarest wildlife, especially birdlife. Among the species seen are mallard, coot, moorhen, great crested grebe, greylag goose, Canada goose, Egyptian goose, grey heron, marsh harrier, cormorant, kestrel, sparrowhawk and bittern. Among the rare insects are the Norfolk hawker dragonfly, and the swallowtail butterfly

The headwaters of the Little Ouse and Waveney valleys hold some of the UK's most precious fens, which are internationally important for rarities such as sundew, bogbean, grass of Parnassus and great raft spider, as well as supporting significant populations of declining bird species, such as reed bunting, and good numbers of water vole.

In the heart of The Fens, the Ouse Washes is a large area of grazing pasture that floods in the winter, attracting thousands of ducks and swans, while hundreds of snipe, lapwings and redshanks breed in the spring.