Orford Ness (above) and Havergate Island will launch the Alde-Ore Estuary conservation project with the windfall from the LIFE+ Nature fund, allowing water levels and habitats to be improved for local wildlife and bird species.
"This is a fantastic opportunity to undertake valuable habitat enhancement work on one of our oldest nature reserves," said Aaron Howe, South Suffolk Reserves Manager for the Royal Society for the Protection of Birds.
"This work will enhance both the habitat for the species found on the reserve and the experience offered to the visiting public."
Orford Ness attracts a host of rare creatures to the site's unusual habitat of vegetated shingle, and a programme created by the scheme will aim to prevent visitors trying to enter fragile areas of the beauty spot.
Stuart Warrington, Nature Conservation Adviser for Orford Ness managers the National Trust, said the deal was "a great boost" to their work.
"The effects of all this work will be closely monitored and evaluated to inform future site management plans," he explained.
"We also know that keeping everyone up to date and informed is vital, so great effort will be put into letting the world know about progress with the project, including a new website and webcams."
The four-year projects will begin in April 2010.