The wildlife site sits on the intersection of both HS2 and East-West Rail, and the BBOWT have expressed anger and disappointment at HS2's lack of planning and accountability.
BBOWT describe the site as "A lakeside sprinkled with wild flowers - a haven for birdwatchers with tufted duck, kingfisher and common tern."
The trust have decided to take direct action, banning contractors from the site "while the notice to proceed has been pushed back" and have asked HS2 to produce a "scheme of works and mitigation that addresses their concerns and respects the needs of wildlife."
In March, Cheryl Gillan MP for Amersham and Chesham took on Nusrat Ghani Parliamentary Under-Secretary for the Department for Transport in the House of Commons and raised serious concerns about the vegetation clearance planned by HS2 at the site during the height of nesting season.
Mrs Gillam asked what steps were being taken to ensure the protection of birds during the breeding season and other wildlife at the protected nature reserve at Calvert Jubilee during ground clearance activities by HS2 Ltd.
At the time, Mrs Ghani responded:
"HS2 Ltd and their contractors will comply with all relevant legislation."
However, the trust are not happy with HS2's behaviour at the site.
Matthew Stanton from the BBOWT said: "The site is a particularly sensitive one because it's placed at a cross section between HS2 and EastWest Rail, both projects will involve destruction of habitats at the site.
"HS2 contacted us last month about clearance works, which we objected to in the strongest terms possible because it would have been at the height of bird nesting season.
"They have looked to push back the works to the summer, but this is still nesting season and unacceptable.
"It's a case of complete mismanagement.
"They should have spoken to us years ago and the mitigation habitats should have been installed up to a a year ago to allow birds and wildlife to settle into the new areas.
"As things stand, they want to rip out the habitat then build them again - in this case where does the wildlife go in the interim?
"We will continue to deny access to HS2 contractors until proper plans are in place to help wildlife flourish."
Speaking at the time, the BBOWT voiced their concerns about the rare animals that live on the site, including five rare species of hairstreak butterflies.
They said: "Regarding Calvert Jubilee, Calvert is particularly known for its warbler assemblage. The scrub mosaic and the lake fringing habitat is good for species such as cetti’s warbler, blackcap, garden warbler and reed warbler.
"Cuckoos are also a specialty on site presumably attracted by host species such as reed bunting and reed warbler. Waterbirds on the lake include common tern and great crested grebe.
Matthew continued: "We've had two meetings with HS2 where we have expressed our concerns for the wildlife at the site.
"They still haven't told us what they are doing, or plan to do. There are no methodologies or clearance work plans, It's all been very poor from HS2.
"There's been a complete communications breakdown and a lack of accountability."
A spokesperson for HS2 said they understood the trust's concerns, and were working to 'minimise impact' of any works taking place.
He said: “We understand some communities along the route are concerned about activity in their area and we are working closely with them, interest groups and the local council, to minimise the impact of our works.
"The works currently being delivered by HS2 Ltd are necessary to build the new railway, and are already supporting over 7,000 jobs through business in the supply chain.
“At Calvert Jubilee we have had meetings with the Wildlife Trust over several years, have shared our Environmental Statement with them, including details of all mitigation work.
"We would like to assure people that all our mitigation work complies with environmental standards, follows established best practice guidelines, and we have met with BBOWT to describe this approach.”
“HS2 is well advanced with the creation of a Green Corridor along the route of the new railway and, so far 350,000 new trees have been planted and 26 areas of new habitat created for wildlife.
"Near to the Calvert Jubilee Nature Reserve, this includes Decoypond Wood in Bernwood Forest where 2,000 trees have already been planted to create a new flight path for a rare species of bat native to the area.
"This is part of a programme of planting which will see 35,000 new trees planted in to improve connectivity between existing habitats in the Calvert area over the next 12 months.”