Vast tracks of forest once blanketed most of the Mixedwood Plains. Areas to the north and east of Toronto were covered in the Great Lakes-St. Lawrence forest region, characterized by Eastern White Pine, Eastern Hemlock, Yellow Birch, and Red Pine. An abundance of broad-leaved species, such as Sugar Maple, Red Oak, Basswood, and White Elm, were also widely distributed throughout the area. A small portion of the deciduous, or Carolinian, forest region reaches its northern limits in southwestern Ontario between lakes Huron, Erie, and Ontario. Tulip-tree, Blue Ash, Red Mulberry, and Kentucky Coffee-tree are confined largely to the warmest portions of the ecozone. These unique deciduous forests are intermixed with Black Walnut, Sycamore, and the more common Great Lakes-St. Lawrence forest species.

Very little of the original forest remains today. Centuries of agriculture, logging, and urbanization in particular, fragmented the landscape into isolated pockets of forest. In Ontario, many of these pockets are now farms, woodlots, urban forests, or protected areas. Heavily forested areas are, however, more common around the northern lakes. Presently, the ecozone's forests consist of 12.8% mixedwood, 2.1% deciduous, and 0.2% coniferous trees.

Even though the Mixedwood Plains represent Canada's smallest terrestrial ecozone, they contain over half the nation's endangered and threatened species. The American Ginseng, designated as threatened by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC), inhabits rich moist deciduous forests in southwestern Quebec and southern Ontario. Populations have been drastically reduced by excessive cattle grazing, logging, and the commercial harvest of its roots. In the late 1980s the Blue-eyed Mary disappeared from open woodland sites along waterways in south-central Ontario.

Influenced by the surrounding Great Lakes and tropical air from the Gulf of Mexico, the Carolinian forests are home to a unique combination of plants and wildlife. Stretching from Windsor in the west to the eastern border of Metropolitan Toronto, this zone represents one of Canada's most vulnerable ecosystems. Today, forest cover ranges from a mere 3 to 16%, and 40% of Ontario's rare plants are restricted to the region. Endangered species include the Prickly Pear Cactus, Small-whorled Pogonia, Cucumber Tree, and Wood Poppy.

Today’s forest ecosystems are decorated with vibrant wildflowers and shrubs. Trilliums, Clover, Black-eyed Susans, Goldenrod, and Wild Raspberry are common. Thickets and abandoned fields give rise to successional species such as Staghorn Sumac, Highbush Cranberry, Red-osier Dogwood, and Willow. Various aquatic species inhabit the few remaining wetlands in the Great Lakes Basin, and along the shorelines of Lake St. Clair, Lake Erie, and the St. Lawrence River. Native and exotic plants, such as cattails, water lilies, sedges, and Purple Loosestrife, can be found in wetlands as well.