Biotic indicators are useful for assessing ecosystem health because the structure of resident communities generally reflects abiotic conditions integrated over time. We used fish data collected over 5 years for 470 Great Lakes coastal wetlands to develop multi-metric indices of biotic integrity (IBI). Sampling and IBI development were stratified by vegetation type within each wetland to account for differences in physical habitat. Metrics were evaluated against numerous indices of anthropogenic disturbance derived from water quality and surrounding land-cover variables. Separate datasets were used for IBI development and testing. IBIs were composed of 10–11 metrics for each of four vegetation types (bulrush, cattail, water lily, and submersed aquatic vegetation). Scores of all IBIs correlated well with disturbance indices using the development data, and the accuracy of our IBIs was validated using the testing data. Our fish IBIs can be used to prioritize wetland protection and restoration efforts across the Great Lakes basin. The IBIs will also be useful in monitoring programs mandated by the Agreement between Canada and the United States of America on Great Lakes Water Quality, such as for assessing Beneficial Use Impairments (BUIs) in Great Lakes Areas of Concern, and in other ecosystem management programs in Canada and the USA.

Planning for freshwater conservation is often secondary to that for terrestrial protected areas and rarely considers all aspects of biodiversity, such as functional biodiversity. To illustrate the application of functional diversity in conservation planning, we used data from a large-scale monitoring program to characterize patterns in functional and taxonomic fish biodiversity across coastal freshwater wetlands in northern Laurentian Great Lakes. We assessed the relationship between these 2 types of diversity to identify areas most likely to maximize conservation benefits in terms of these dimensions of biodiversity. In addition, we used an outlier analysis to find areas with unexpectedly high taxonomic or functional diversity in highly impacted watersheds, or bright spots. Taxonomic and functional fish diversity metrics were not closely related, and different areas across the basin supported highest taxonomic and functional diversities. Several bright spots had either very high taxonomic richness or functional diversity despite intensive anthropogenic land use, possibly indicating high resilience and conservation potential. These findings are relevant in the context of freshwater protected area prioritization because there are few guidelines available for nomination and selection of new freshwater protected areas.