About 70 percent of the Altamaha Basin's land area is covered with forest. In the Coastal Plain region the woodland, part of the Southeastern Pine Forest of the U.S., is dominated by slash and longleaf pine. Large areas of natural forest have been replaced by managed plantations of loblolly pine. Hardwood trees, notably the large live oak, are intermixed with pine. Swamp trees, such as cypress and tupelo, and marsh grasses grow in some low-lying areas. The forest in the Piedmont region is mainly a mixture of oak and pine.

The Altamaha River Basin is home to several unique plant species and a number of protected native plants. As human impacts increase in the watershed some species are threatened or destroyed, while conditions favor the spread of invasive and introduced plant species.