Saugus Iron Works National Historic Site contains over 160 species of plants. Approximately 89 species of these plants are considered native to the area. Several species of trees can be found along the Saugus River within the riparian woodlands. Examples include white and scarlet oaks, American beech, shagbark hickory, black walnut, black cherry, black willow, red and silver maples, and boxelder. Many of these trees provide food to the native birds, squirrels, and chipmunks by producing seeds and nuts.
At least 27 species of plants are found within the wetland areas surrounding the Saugus River. Many of these plants are common throughout the marsh, such as narrow-leaved cattail. The tall wetland vegetation provides excellent habitat for nesting red-wing blackbirds and other bird species and breeding fish, such as the fourspine stickleback.
Wildflowers are also abundant throughout the year at Saugus Iron Works. Jack-in-the-pulpit, skunk cabbage, jewelweed, goldenrod, and several species of asters can be found throughout the historic site. Saugus Iron Works is also home to three species of fern: sensitive fern, cinnamon fern, and lady-fern.