The Donna Nook range near Mablethorpe is an active bombing range, but also a haven for grey seals, rare orchids, wading birds and natterjack toads.
On Thursday, the site is being made part of English Nature's network of reserves aimed at protecting the most important wildlife habitats in the country.
Because the reserve - 10km (6.25 miles) of coastline between Grainthorpe Haven in the north and Saltfleet in the south - is closed off for much of the week, the creatures are undisturbed by people.
The military restrictions have also helped preserve their habitat.
The MoD has been working with local volunteers from the Lincolnshire Wildlife Trust to help manage the site.
Stuart Crooks, director of the trust, said Donna Nook was a "dynamic landscape" and "one of the few truly wild places left in Lincolnshire".
'Magical ribbon'
Squadron Leader Neil Jones said: "By far the most visible aspect of the Donna Nook reserve is the colony of grey seals, which is resident here.
"They're gregarious and live quite happily in family groups in the sand flats, totally unconcerned about the activities on the bombing range."
Dr Andy Brown, acting chief executive of English Nature, said: "Donna Nook is the fourth national nature reserve on the Lincolnshire coast which together form a magical ribbon of sand dunes and mudflats that provide food and a place to nest for many different birds.
"Pyramidal orchids, shy wading birds and sweeping sand dunes make Donna Nook exactly the kind of place that deserves to be a National Nature Reserve."
There are now 213 national nature reserves in England covering more than 86,000 hectares.