Air pollution is damaging 60% of Europe's prime wildlife sites in meadows, forests and heaths, according to a new report.
A team of EU scientists said nitrogen emissions from cars, factories and farming was threatening biodiversity.
It's the second report this week warning of the on-going risks and threats linked to nitrogen pollution.
The Nitrogen Deposition and Natura 2000 report was published at a key scientific conference in Edinburgh.
Earlier this week, the European Nitrogen Assessment - the first of its kind - estimated nitrogen damage to health and the environment at between £55bn and £280bn a year in Europe, even though nitrogen pollution from vehicles and industry had dropped 30% over recent decades.
Nitrogen in the atmosphere is harmless in its inert state, but the report says reactive forms of nitrogen, largely produced by human activity, can be a menace to the natural world.
Emissions mostly come from vehicle exhausts, factories, artificial fertilisers and manure from intensive farming.
The reactive nitrogen they emit to the air disrupts the environment in two ways:
It can make acidic soils too acidic to support their previous mix of species.
But primarily, because nitrogen is a fertiliser, it favours wild plants that can maximise the use of nitrogen to help them grow.
In effect, some of the nitrogen spread to fertilise crops is carried in the atmosphere to fertilise weeds, possibly a great distance from where the chemicals were first applied.
The effects of fertilisation and acidification favour common aggressive species like grasses, brambles and nettles.
They harm more delicate species like lichens, mosses, harebells and insect-eating sundew plants.
'Ignored problem'
The report said 60% of wildlife sites were now receiving a critical load of reactive nitrogen.
The report's lead author, Dr Kevin Hicks from the University of York's Stockholm Environment Institute (SEI), told BBC News that England's Peak District had a demonstrably low range of species as a result of the reactive nitrogen that fell on the area.
"Nitrogen creates a rather big problem that seems to me to have been given too little attention," he said.
"Governments are obliged by the EU Habitats Directive to protect areas like this, but they are clearly failing."
He said more research was needed to understand the knock-on effects for creatures from the changes in vegetation inadvertently caused by emissions from cars, industry and farms.
At the conference, the delegates agreed "The Edinburgh Declaration on Reactive Nitrogen".
The document highlights the importance of reducing reactive nitrogen emissions to the environment, adding that the benefits of reducing nitrogen outweigh the costs of taking action.
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