The country’s largest wetland and protected northern moors are among the habitats at stake if ministers cannot agree on a deal before the end of March.
Frustrated after failed attempts to block roads being built through swan-nesting grounds or the burning of bogs to create shooting estates, many local groups have turned to Europe for help.
There are currently 14 active cases from Britain involving potential breaches of environmental laws listed by the European Commission, with more thought to be in the pipeline.
As part of its “green Brexit” vision, the government plans to create a new body to replace the commission and the European Court of Justice (ECJ), which are capable of holding states to account for their environmental shortcomings.
The EU has taken the UK to court more than 50 times over its poor efforts to protect nature, forcing it to clean up the air and protect porpoises in its waters.
But with exit day only two months away, experts think there will be little political will from either European or British authorities to continue ongoing proceedings if no deal is agreed.
“I don’t see why first the commission would keep on spending time and effort on these cases, and second why the UK government would listen if anything came out of them,” said Dr Viviane Gravey, an expert in EU environmental policy at Queen’s University Belfast.
Lawyers in Brussels are currently investigating Lough Neagh and Lough Beg in Northern Ireland, the largest wetlands in the British Isles and home to nesting whooper swans.
Campaigners have exhausted all other routes to oppose a planned road through Lough Beg’s floodplain and controversial sand mining taking place on Lough Neagh.
However, given its designation as a special protected area under EU law, they were able to take their case to the commission. Now, with the case still hanging in the balance, they fear time has run out.
“A no deal means no access to a complaints procedure that could be all that stands between this area being the jewel of Northern Ireland’s crown or a desecration of a unique landscape,” said James Orr, director of Friends of the Earth Northern Ireland.
Another complaint involving attempts to burn dozens of blanket bogs in the north of England and turn them into shooting estates has been underway for six years.
After submitting a case to the commission, conservation groups achieved victory in 2018 when the government agreed to preserve these unique habitats.
However, with a deadline of June to end the burning on grouse hunting estates, a no-deal outcome in March could compromise years of struggle.
“It remains to be seen whether they achieve it… we are pessimistic that the moment,” said Andrew Dodd, who has worked on the case for the RSPB.
“The commission’s involvement is critical to ensure [the government] delivers, and if we don’t have a transition period it’s going to be down to the likes of RSPB and other NGOs to keep on pushing the UK government.”
A spokesperson from the commission confirmed that while legal proceedings would be brought to a conclusion under the withdrawal agreement, they could not speculate about a no-deal scenario.
If recommendations by the commission do not persuade a nation to make changes, the case will pass to the ECJ as the final arbiter.
Dr Gravey said owing to the bad press the commission and the ECJ tend to get in the UK, there is unlikely to be any political fallout for the government in ignoring their rulings.
“In certain circumstances we’ve seen how European institutions can be quite literally the last line of legal defence for environmental cases in the UK,” said Dr Tom West from environment lawyers ClientEarth, noting that Michael Gove’s proposed environmental watchdog will not be ready in time for an emergency no deal.
A spokesperson for the Department for Environment, Food and Rural Affairs said: “We are fully committed to pursuing an orderly, negotiated withdrawal from the European Union. However, as a responsible Government we are also preparing for no deal, including the implications this would have for the current infractions process.
“We will not weaken environmental protection when we leave the EU, but will instead maintain – and even enhance - our already high environmental standards.”