HS2 has taken over Calvert Jubilee -'an incredibly sad day for wildlife'
Berks, Bucks and Oxon Wildlife Trust said they were 'absolutely devastated' by the news.
HS2 Ltd has now taken legal possession of a large section of the Calvert Jubilee Nature Reserve.
Anti-HS2 protestors who had set up camp have been removed from the site by security guards and police.
HS2 has a warrant for the site so officially has taken over.
Despite HS2 assuring the Berks, Bucks and Oxon Wildlife Trust (BBOWT) it would give notice of when it would take possession, the trust says it 'moved onto site without informing us.'
A BBOWT spokesman said: "Construction workers will destroy decades of hard work by BBOWT staff and volunteers who have made the site a haven for wildlife.
"An area on the eastern side of the reserve will be flattened to make space for the railway.
"Calvert Jubilee is one of the jewels in the crown of our nature reserves - a peaceful lakeside sprinkled with wild flowers and a quiet haven for wildlife and people."
Over the last 50 years, the reserve has become a haven for large numbers of overwintering waterfowl and waders.
Birds like blackcap nest in the trees and scrub, and the reeds in the shallower parts of the lake play host to the bittern.
The site is renowned as a home to all five species of UK hairstreak butterfly.
The trust spokesman added: "This fabulous matrix of habitats is a direct result of the hard work and passion of the people who have made Calvert Jubilee a real gem for wildlife. We are devastated that an area of this beautiful place will be lost to HS2 and much of what remains of the reserve will be overshadowed by the huge infrastructure project."
BBOWT’s head of planning, policy and advocacy, Matthew Stanton, said: “We are devastated that HS2 have now taken possession of a huge part of our Calvert Jubilee Nature Reserve.
“They will fence it off, clear it and destroy decades of hard work by BBOWT staff and volunteers to make it a haven for wildlife.
“We have fought HS2 from the beginning and are grateful to everyone who has helped to try and stop, and at least delay, this sad day arriving.”
Mark Vallance, reserves manager for Buckinghamshire said: "I am heartbroken to know that HS2’s chainsaws and diggers will destroy habitats that have been looked after by dedicated people for more than 40 years on one of our most diverse and beautiful nature reserves.
“I grew up a few miles from Calvert Jubilee - my visits there as a young boy set me on the path to my career today. The areas that will be destroyed by HS2 have given me some amazing wildlife experiences over the years, including the incredible sight and sound of the elusive and rare nightingale.
“This is an incredibly sad day for wildlife.
"We have refused HS2 and its contractors access to Calvert Jubilee at every opportunity and we continue to oppose all clearance works, particularly any that are proposed to take place during bird nesting season. But in spite of our best efforts and our vigorous campaigning, an area of this precious nature reserve will be destroyed forever.
"BBOWT have campaigned against HS2 ever since it was proposed."