We collected water quality, land use, and aquatic macrophyte information from 62 coastal and inland wetlands in the Great Lakes basin and found that species richness and community structure of macrophytes were a function of geographic location and water quality. For inland wetlands, the primary source of water quality degradation was inputs of nutrients and sediment associated with altered land use, whereas for coastal wetlands, water quality was also influenced by exposure and mixing with the respective Great Lakes. Wetlands within the subbasins of the less developed, more exposed upper Great Lakes had unique physical and ecological characteristics compared with the more developed, less sheltered wetlands of the lower Great Lakes and those located inland. Turbid, nutrient-rich wetlands were characterized by a fringe of emergent vegetation, with a few sparsely distributed submergent plant species. High-quality wetlands had clearer water and lower nutrient levels and contained a mix of emergent and floating-leaf taxa with a diverse and dense submergent plant community. Certain macrophyte taxa were identified as intolerant of turbid, nutrient-rich conditions (e.g., Pontederia cordata, Najas flaxilis), while others were tolerant of a wide range of conditions (e.g., Typha spp., Potamogeton pectinatus) occurring in both degraded and pristine wetlands.