The French Creek Watershed is located within the Northern Hardwood Forest community characterized by dominant species that includes sugar maple (Acer saccharum), American beech (Fagus grandifolia), and eastern hemlock (Tsuga canadensis) interspersed with white pine (Pinus strobus) and oaks (Quercus spp.). Lakes and marshes created during glaciation, along with intensive timbering and agricultural clearing in the 19th and 20th centuries, have created farmland, grassland, old-field and wetland habitats supporting an array of diverse plant communities.

Numerous rare and endangered species are found in the watershed, including the showy lady’s slipper (Cypripedium reginae), a threatened species in Pennsylvania. Wetlands surrounding Lake Pleasant, located near the town of Waterford, provide habitat for more than twenty plant species of special concern in the state, including northern water milfoil (Myriophyllum sibiricum), rush aster (Aster borealis) and cuckoo-flower (Cardamine pratensis). Lake Pleasant also has two fish species, the blackchin shiner (Notropis heterodon) and Iowa darter (Etheostoma exile) that are endangered in the state. The largest bottomland forest in the Pennsylvania headwaters is found in the South Branch sub-basin, also a home to rare plant species in its fens and seeps.