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Coastal wetlands of the Laurentian Great Lakes are vital habitats for biota of ecological and economic importance. These habitats are susceptible to water quality impairments driven by runoff from the landscape due to their location along the shoreline. Monitoring of the overall status of biotic and abiotic conditions of coastal wetlands within the Great Lakes has been ongoing for over a decade. Here, we utilize measurements of aquatic physicochemical and land cover variables from 877 vegetation zones in 511 coastal wetland sites spanning the US and Canadian shorelines of the entire Great Lakes basin. Our objective is to develop water quality indices based on physicochemical measures (Chem-Rank), land use/land cover (LULC-Rank), and their combined effects (Sum-Rank and Simplified Sum-Rank), for both vegetation zones and wetland sites. We found that water quality differed among wetland vegetation types and among Great Lakes regions, corroborating previous findings that human land use alters coastal wetland water quality. Future monitoring can use these straightforward, easy-to-calculate indices to assess the abiotic condition of aquatic habitats. Our data support the need for management efforts focused on reducing nutrient and pollution loads that stem from human activities, particularly in the developed southern portions of the Great Lakes basin.