Indices such as the Index of Biotic Integrity (IBI) are often used by management agencies to estimate the abstract property of stream health. These indices are usually predicated on the belief that certain fish species are tolerant to environmental perturbation while others are sensitive. Species are usually designated as either tolerant or sensitive in these analyses based on inherent ecological or taxonomic characteristics. However, previous literature has shown that certain species from ecological or taxonomic “sensitive” groups experience increased abundance in degraded streams. We term such species “cryptic tolerants”. Using a stream fish assemblage dataset of 433 unique sample locations across the state of Alabama and the National Landcover Dataset, our objectives were to 1) identify the most common cryptic tolerant species, 2) investigate how cryptic tolerant species might inflate indices of stream health, and 3) compare an alternative measure of stream health in which species are statistically defined rather than defined using the traditional trait-based approach. We identified cryptic tolerants using Nonmetric Multidimensional Scaling in six ecoregions. A series of regressions revealed that the proportion of cryptic tolerant species decreased in response to an increasing proportion of forested land in catchments while the proportion of true sensitives increased in all ecoregions except for the Cumberland Plateau. An index that simply used the percentage of statistically defined, non-tolerant species generally had lower p-values and higher r² values than IBI scores when both were regressed against percentage of forest in catchment. However, both indices had low degrees of correlation with expected disturbance, indicating a univariate index may be inadequate to characterize stream health. Our results highlight a potential issue with applying the IBI to diverse southeastern systems in the United States, which may be alleviated by designating species sensitivity based on empirical response to disturbance rather than taxonomic or ecological characteristics.