Surge tide flood waters have damaged part of a breeding ground used by rare species of birds, the RSPB has said.
Bitterns had to be reintroduced to the UK
Reedbeds at Dingle Marshes in Suffolk and neighbouring Walberswick National Nature Reserve - both prime habitat for the bittern - have been flooded.
Salt water has inundated freshwater beds at the RSPB's Strumpshaw Fen in the Norfolk Broads.
This has killed large numbers of fish and reduced the likelihood of bitterns breeding there next year.
But other key reserves in Essex had a lucky escape as the surge tide was not so strong.
"This has been a close run thing, but sea levels are rising and storms are only going to become more frequent as our climate warms," said Dr Mark Avery, the RSPB's director of conservation.
"This whole coast is of huge value for wildlife, covered in sites of international importance and it is imperative the Government acts now to create the habitat plants and animals are going to need if they are to survive in a changing world."
Meanwhile the RSPCA rescued 26 cows from a heavily flooded field in Beccles, Suffolk.
The Limousin breed of cattle were spotted in several feet of water on Friday afternoon.
RSPCA inspectors used an inflatable dinghy to reach the animals and coax them to dry land.