We developed an index of biotic integrity (IBI) based on crayfish, fish, and amphibian assemblages to assess vernal ponds and palustrine wetland habitats of less than 5 ha along the southern shore of Lake Michigan. We found that the modified IBI based on three crayfish, twelve fish, and seven amphibian species collected during our surveys provided a more complete assessment than one based on any single taxonomic group. The new scoring criteria included the number of amphibian and fish species, number of benthic species, percent of individuals as pioneer species, percent of individuals as exotic species and percent of individuals with complex reproductive modes for metrics developed for larger palustrine wetlands. Low-end scoring procedures were not required; however, species composition metrics that did not possess the specified attribute received a ‘0’ score rather than a ‘1’. Correlation coefficients suggest that the reference conditions developed during this study of IBI metrics are able to differentiate high-quality biological assemblages from disturbance gradients that lowered biological integrity in small palustrine wetlands and vernal ponds. We found that the distribution of the index scores for Miller Woods was skewed to the low end of biological integrity with increased distance from Lake Michigan and proximity to edges.