The Nine Mile Run Area contains a mosaic of vegetation types, heavily influenced by the activities of man over many decades, including remnants of native vegetation types to areas almost completely devoid of plant growth. Six basic vegetation types occur in the Nine Mile Run area: Riparian and Flood Plain, Forest, Grassland, Slag Plateaus, Vegetated Slag Slopes, and Bare Slag Slopes. Within all six of these vegetation types, both introduced and native plants occur, although in different proportions.

 Plants at Nine Mile Run: Many of the plant species found at Nine Mile Run are introduced European and Eurasian weeds, but a substantial proportion are species that are native to this area, including many native "weedy" species. The native weed species play an important role in normal successional growth and include species, such as staghorn sumac (Rhus typhina) and black locust (Robinia pseudoacacia), that colonize bare open areas. In areas of Nine Mile Run, these plants compete with introduced successional species, such as the tree of heaven (Ailanthus altissima), which can even grow through cracks in sidewalks!

 Relatively undisturbed forest areas contain native hardwoods, such as the tulip-tree (Liriodendron tulipifera), basswood (Tilia americana), various species of oaks (Quercus spp.), and sugar maple (Acer saccharum) and a mixture of introduced and native species in the understory and forest floor. There are also some invasive species at Nine Mile Run; Garlic Mustard (Alliaria officinalis), Japanese Honeysuckle (Lonicera japonica), Crown vetch (Coronilla varia) and Japanese Knotweed (Polygonum cuspidatum). Invasive species are not only hardy but also spread rapidly, taking area from native plant colonies. The dynamics of this mixture must be monitored to maintain this vegetation type within Nine Mile Run.