Fish community composition often varies across ecoregions and hydrogeomorphic types within ecoregions. We evaluated two indices of biotic integrity (IBIs) developed for fish in Great Lakes coastal wetlands dominated (> 50% cover) by Typha (cattail) and Schoenoplectus (formerly Scirpus) (bulrush) vegetation. Thirty-three coastal wetlands dominated by either Typha or Schoenoplectus vegetation were sampled using fyke nets set overnight. These sites were selected to span anthropogenic disturbance gradients based on population density, road density, urban development, point-source pollution, and agricultural inputs (nutrients, sediments), measured using a GIS-based analysis of Great Lakes coastal land use. Sites subject to low levels of anthropogenic influence had high IBI scores. The Typha-specific IBI showed a marginally significant negative correlation with population density and residential development (r = −0.54, p < 0.05; n = 21). The Schoenoplectus-specific IBI negatively correlated most strongly with nutrient and chemical inputs associated with agricultural activity and point-source pollution (r = −0.66 and −0.52, respectively; p < 0.01; n = 30). However, some relationships between IBI and disturbance scores were non-linear and likely exhibit a threshold relationship, particularly for Schoenoplectus dominant sites. Once a certain level of disturbance has been exceeded, a sharp change in fish community's composition and function occurs which is symptomatic of a degraded site. The IBI indices appear to indicate effects of some, but not all classes of anthropogenic disturbance on fish communities. Calibrating these measures against specific stress gradients allows one to interpret the sources of impairment, and thereby use the measures beyond a simple identification of impaired sites.