At least nine species of native mammals have been observed within Saugus Iron Works National Historic Site. The most common mammal found here is the eastern gray squirrel (Sciurus carolinensis) where it can be seen daily throughout the year within the riparian woodlands and the landscaped areas surrounding the historic buildings. Two other mammals that are closely related to the eastern gray squirrel can also be seen within Saugus Iron Works, the eastern chipmunk (Tamias striatus) and the woodchuck (Marmota monax).

Several species of mammals depend upon the Saugus River as an important habitat and food source. The muskrat (Ondatra zibethica), raccoon (Procyon lotor), and river otter (Lutra canadensis) can be occasionally seen within the river and surrounding marshes.

Other mammals that have been observed within Saugus Iron Works include deer mice (Peromyscus maniculatus), striped skunks (Mephitis mephitis), mink (Mustela vison), and bats (Chiroptera).