A project to improve conditions of tens of thousands of hectares in the River Tweed area and along the Northumberland coast will receive £5.8 million of EU funding.
It aims to support key over-wintering birds such as the purple sandpiper, as well as Arctic tern breeding colonies, which help control invasive species and improve visitor management. The scheme will benefit more than 49,000 hectares (120,000 acres) of habitat and water quality.
It is part of an £11 million pot split over three projects in Northumberland and the Scottish Borders, Cumbria, and South Yorkshire. The three plans over the next five years are aimed at tackling the nature and climate crises, government conservation agency Natural England said.
One of the other projects is a conservation scheme in Cumbria, to increase the population of critically endangered freshwater pearl mussels along parts of the River Kent in the county, which is receiving £3.8 million.
The threatened mussels can filter up to 50 litres of water a day, improving the water quality for species such as fish, eels and otters.
The third plan aims to restore and improve 400 hectares (1,000 acres) of degraded raised bogs and trial innovative payment schemes for carbon storage in the Thorne Moor Special Area of Conservation in South Yorkshire.
The scheme, focusing on the largest area of carbon-rich lowland raised peatbog in England, one of western Europe's rarest and threatened habitats, is receiving £2.1 million.
They will be delivered in partnerships led by Natural England and funded by EU Life, having bid for funding from the European conservation scheme before it closed to British projects.
Natural England chairman Tony Juniper said: "These innovative partnership projects present highly tangible examples of the efforts being made to protect and restore critically endangered species and habitats.
"From the conservation of freshwater pearl mussels in Cumbria to storing carbon in lowland raised bog in South Yorkshire, these new nature recovery projects are among a series of initiatives through which Natural England is taking the lead in tackling the biodiversity crisis and climate change challenge.
"I'm hopeful that these nature recovery projects will inspire more action across the country, enabling more people to enjoy wildlife-rich natural landscapes into the future."