Of primary significance at Wabikon Lake are the extensive high-quality forested wetlands with several rare plant populations. Along the shore of Wabikon Lake is an old-growth hemlock stand with occasional sugar maple, yellow birch, and white cedar present. The hemlock ranges from pole-size to at least 34 inches in diameter. The dense shade of the hemlock results in a very sparse, nearly absent, groundlayer. Extensive swamp forests in the northeast quarter occupy an area that was formerly part of Wabikon Lake and are partly underlain by lacustrine sands. These stands vary in quality and composition, ranging from the excellent old-growth white-cedar in the east-central part of the complex, to a large "hybrid" swamp containing both black spruce bog and white-cedar swamp components in the northeast quarter. Black ash is common to dominant in some stands, with red maple and yellow birch also common. The shallow waters along the shores of both Wabikon and Riley Lakes contain extensive high-quality emergent aquatic communities.

The bulrushes, cattails, and large wild-rice patches attract numerous waterfowl. Water-willow is abundant in a floating sedge mat on Riley Lake as well as along the channel connecting the two lakes. In the western half of the complex are mixed northern hardwood forests on hummocky terrain dominated by sugar maple and basswood. White ash is prominent in some stands, while yellow birch is scattered throughout. Black cherry, butternut, red oak, and mature aspen are occasional to frequent. American elm was formerly an important component but now survives only as saplings due to the introduction of Dutch elm disease. The understory varies from open to dense, with thick stands of sugar maple and white ash saplings occurring in places. Eastern hop-hornbeam is fairly common. Common groundlayer species include maidenhair fern, large-flowered bellwort, plantain-leaved sedge, and American spikenard. A prominent esker running discontinuously north to south through the center of the complex supports a mix of CCC-planted white spruce, young aspen stands, fir, and mixed hardwoods. Soils here are rockier and appear less fertile than those to the west. Groundlayers are also not as rich and are quite sparse under the dense white spruce. A large recent blowdown caught the north edge of the complex and cut an approximately 1/8 mile-wide swath in the forest, reaching the shore of Wabikon Lake and perhaps beyond. The portion of the blowdown on FS land is unsalvaged and exhibits excellent hardwood regeneration, as compared to the salvaged private land to the north. Wabikon Lake is owned by the US Forest Service and was designated a State Natural Area in 2007.