Centuries of forestry, agriculture, and natural disturbances have left few pockets of old-growth forest. Today, forests are predominantly secondary and tertiary growth on old clear-cuts and abandoned farms. Decades of logging are also responsible for habitat destruction, soil erosion, and increased nutrient loss.

The Atlantic Maritime Ecozone ranks as the third most forested ecozone with 76% of its surface area covered with forests, which are divided into three distinct regions: Boreal, Great Lakes-St. Lawrence, and Acadian. The Boreal region, associated with fir and spruce, stretches from the northwestern tip of New Brunswick into the Gaspé Peninsula. Eastern White Pine, Red Pine, Yellow Birch, and Eastern Hemlock typify the relatively small Great Lakes-St. Lawrence region of northern New Brunswick. Acadian forests, covering 44% of the entire ecozone, are characterized by a mixture of coniferous and deciduous species. Hardwoods, such as Sugar Maple, Beech, and Yellow Birch, dominate shallow but well-drained slopes and hillsides. Conifers, especially Red Spruce, are concentrated in moist soils, coastal fringes, and areas recovering from disturbances. All three regions are interlaced with numerous lakes and wetlands.

Moss, lichen, ferns, and heathers are typical of swampy areas and rocky barrens. Seaweed and kelp grow along exposed coastlines. Acadian forests are decorated with wildflowers such as Trailing Arbutus, Lady Slipper, Pitcher Plant, and several varieties of violets. The Ostrich Fern, harvested for its fiddlehead in the spring, thrives on deciduous-covered streambanks in New Brunswick and Nova Scotia. Blueberry, Pin Cherry, and Speckled Alder are also common. The Purple Loosestrife, an introduced species, has proliferated and displaced many native wetland species.

At least 10 plants are recognized as either endangered or threatened by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). The endangered Water-pennywort, a small creeping species of tropical origin, is limited to two localities in southeastern Nova Scotia. Cottage development and recreational activities have placed the Water-pennywort at risk. The Furbish's Lousewort grows exclusively along a 200-kilometre stretch of the Upper Saint John River in New Brunswick. Habitat destruction due to farming, forestry, and flooding from hydro-electric development has put the Furbish's Lousewort on the endangered list.

The Spruce Budworm has significantly influenced the ecozone's forests. The most recent outbreak, beginning in the late 1960s, either destroyed or severely damaged large expanses of spruce forests. Fortunately, the budworm population has collapsed since 1991 in all but northern New Brunswick. Other species, such as Jack Pine, have taken advantage of the blight, forest fires, and other disturbances.