Using a newly modified index of biotic integrity for assessing biological integrity of fish communities in dunal, palustrine wetlands, we assessed the non-point source influence of an industrial landfill on the Grand Calumet Lagoons. The landfill is primarily an iron and steel manufacturer’s slag waste. No sensitive species, hybrids, headwater species, and either few or no simple lithophilic spawning species were collected from any of the sites in the Grand Calumet Lagoons. Species catch-per-unit of effort varied significantly between reaches in the Middle Lagoon and the West Lagoon. The most disturbed areas were adjacent to the industrial landfill and along the southern shore near the outflow from the West Lagoon. Near- and far-field stations possessed similar numbers of species and relative abundance. The near-field stations showed an increase in tolerant species, a higher proportion of omnivores and carnivores, and a lower environmental quality rating of ‘poor–very poor’. The far-field sites were classified as having ‘fair’ biological integrity and showed an increase in relative abundance, proportion of sensitive species, and an increase in simple lithophils. The loss of biological integrity in the West Pond was not accurately predicted using the modified index of biotic integrity, even though it was rated as extremely degraded by the biological diversity indices. Fish communities were negatively impacted by proximity to the landfill.