Indices have been developed with invertebrates, fish, and water quality parameters to detect the impact of human disturbance on coastal wetlands, but a macrophyte index of fish habitat for the Great Lakes does not currently exist. Because wetland macrophytes are directly influenced by water quality, any impairment in wetland quality should be reflected by taxonomic composition of the aquatic plant community. We developed a wetland macrophyte index (WMI) with plant presence/absence data for 127 coastal wetlands (154 wetland-years) from all five Great Lakes, using results of a canonical correspondence analysis (CCA) to ordinate plant species along a water quality gradient (CCA axis 1). We validated the WMI with data collected before and after the implementation of remedial actions plans (RAPs) in Sturgeon Bay (Severn Sound) and Cootes Paradise Marsh. Consistent with predictions, WMI scores for Sturgeon Bay were significantly higher after the implementation of the RAP. Historical data from Cootes Paradise Marsh were used to track the declining condition of the plant community from the 1940s to 1990s. Subsequently, when remedial actions had been implemented in 1997, the calculated WMI scores showed improvement, but when the presence of exotic species (WMIadj) was accounted for, improvements in ecological integrity of the aquatic-plant community were no longer evident. We show how WMI scores can be used by environmental agencies to assess the historic, current, and future ecological status of wetland ecosystems in two Canadian national parks, Point Pelee National Park (PPNP) and Fathom Five National Marine Park (FFNMP).