Two invasive shrub species are a major concern in Muskego's forests: Tatarian Honeysuckle (Lonicera tatarica) and European Buckthorn (Rhamnus cathartica). Both of these plants were originally brought to North America for use as landscape plants but now spread into forests over much of the continent. These species leaf out sooner than most native woodland trees. Native woodland flowers such as Jack-in-the-Pulpit (Aerisaema trifollium), Trilliums (Trillium grandiflorum), Bloodroot (Sanquinana canadensis), and Mayapple (Podophyllum peltatum) flourish in the sunlight that comes through the forest canopy in spring before the trees leaf-out. Shade from invasive shrubs inhibits the growth of these native plants on the forest floor. Not only are humans robbed of the chance to witness a spectacular display of spring flora, the wildlife that relies on the native species for food and habitat is greatly impacted. This shading effect also inhibits the regeneration of forest trees and, over time, the area can transform into a dense thicket of these invasive shrubs.

Garlic Mustard (Alliaria petiolata), another invasive non-native plant, is a serious threat to the health of the woods in Muskego. This prolific biennial herb can quickly dominate the ground flora of a forest at the expense of the diverse assemblage of native woodland flowers. In the first year it is generally low growing, does not form flowers, and remains green through winter. Second-year plants grow 1-2 feet tall and produce clusters of white blossoms in May and June. Each plant dies after flowering.

Invasions of garlic mustard in Muskego's woodlands range in severity. When garlic mustard infestations are isolated, early control can keep this invader from gaining a foothold and disrupting the forest ecology.