The group said water protection zones (WPZs) were not being used to stop pollution washing into waterways.
It came after Poole Harbour in Dorset and the River Mease in the Midlands were identified as suffering from significant agricultural pollution.
After reassurances that WPZs were being considered, a settlement was agreed.
WWF-UK, the Angling Trust and Fish Legal had accused the Department for Environment, Food and Rural Affairs (Defra) and the Environment Agency of unlawfully keeping WPZs – which can include criminal sanctions for breaches – “on the back burner as a last resort”.
‘Proper measures’
Judge Mr Justice Collins said: “It is obviously of the greatest importance that proper measures are taken as soon as possible to meet the obligations of the directive.”
The organisations joined together to bring the High Court challenge after the government admitted it would not meet a December 22 deadline to ensure the rivers were in good health.
They said they hoped to ensure the protection of 44 “precious” rivers and wetlands England.
The Department for Environment, Food and Rural Affairs (DEFRA) said English rivers were the “healthiest” for 20 years.
A Defra spokesman said: “We are pleased to have reached agreement in this case and we will continue to consider how we use water protection zones as one of the ways to protect our most treasured conservation areas.
“We are committed to working closely with the farming community and environmental groups to further improve water quality.”
