The group is announcing the acquisition today, adding that it has protected 417 hectares in the area, making it one of the largest conservation areas on the Northumberland Strait.
It says the area is home to several bird species, including black ducks, common mergansers and bufflehead.
The estuary is also a habitat for fish during spawning and rearing, while ponds provide water sources for mammals and forest birds.
The conservation group says the project was funded by federal and provincial programs, and local donors.
Craig Smith, the group's program manager in Nova Scotia, says the conservation lands at Pugwash Estuary represent one of two significant protected sites along the Northumberland Strait.