Farmers of lowland cattle and sheep were suffering such drops in income that they could no longer afford basic environmental management, such as hedge maintenance and tree-planting.
Some were going out of business, and grassland that needed grazing to keep its wildlife value was being abandoned, while others were under extreme pressure to plough up grassland and plant crops.
"Our pastoral system, the mixture of lovely countryside with cattle and sheep, is now under real threat," said Ben Gill, the NFU president.
Thousands of farmers and their families are to demonstrate about their financial crisis at the start of the Labour party conference in Blackpool, a week tomorrow.
The NFU had surveyed 1,000 lowland livestock farmers and found that 97 per cent had maintained or increased their hedgerows over the past three years, 67 per cent had planted trees, and 36 per cent had planted new hedges.
In addition, last year 85 per cent of lowland farmers saw a fall in their income and 24 per cent have already been forced to reduce farm labour.
"If this issue is not addressed, wildlife and ecosystems will be destroyed," he said.
He was backed by John Cousins, agricultural policy director of the 300,000- member Wildlife Trusts, who said: "As the beef crisis continues, the future of our finest wildlife habitats hangs in the balance as many need sympathetic grazing to survive."
Mr Gill said farmers had never experienced such pressure were under at the moment. He called for urgent government action to lower interest rates, reduce the value of sterling and lift the beef export ban.
This week he told Stephen Byers, Chief Secretary to the Treasury, that more than half the farmers in England and Wales would not make a profit this year - and the figure for lowland cattle and sheep farmers was likely to be higher.
Mr Byers had replied that interest rates and the pound might fall next year. "I told him that next year is too late as many of my members won't be in business then," Mr Gill said.
Introducing an NFU report, Landscape In Peril, Mr Gill said: "It is not an exaggeration to say that the landscape is now in peril.
"It is a common misunderstanding that trees are there by chance and will look after themselves, and that the hedges that surround the field just look after themselves, too.
"But to maintain the countryside needs active management, and without it there are severe consequences, which are already beginning to show."
Mr Cousins said that the partnership between farming and the environment was often forgotten. "These two elements go hand in hand, and much of our wildlife is actually there because of farming, and the landscape we look at has been created because of farming," he said.
In the lowland areas, grasslands were becoming pressurised and less common, and changes were happening.
The Wildlife Trusts did not believe that lowland grasslands should be abandoned and "left to nature" because they would degrade in conservation terms, become covered by scrub and lose many of their wildflowers, butterflies and birds.
English Nature, the Government's wildlife agency, and the Royal Society for the Protection of Birds associated themselves with the NFU report.