The refuge is located on Maryland's Eastern Shore, just 12 mi (19 km) south of Cambridge, Maryland in Dorchester County, and consists of over 28,000 acres (110 km2) of freshwater impoundments, brackish tidal wetlands, open fields, and mixed evergreen and deciduous forests.

Blackwater Refuge is home to a variety of mammals, which until recently included the South American nutria.

Introduced to the refuge in the 1930s, intensive trapping efforts starting in 2002 helped nearly eliminate the animal from the area.

Blackwater National Wildlife Refuge also offers a wealth of recreational and visitor opportunities for all age groups.

Although much of Blackwater Refuge is composed of wetlands, there are still many ways to get close to the wildlife and to enjoy the scenery.

The staff at the Visitor Center also offer educational programs for children, as well as frequent organized bird walks and an annual Eagle Festival.

There is a daily permit fee of $3.00 for private vehicles (not including commercial vans or buses) and of $1.00 for pedestrians and bicyclists wishing to access the Wildlife Drive.

About half of the refuge is designated the Harriet Tubman Underground Railroad National Monument.