We evaluated the relationship between the fish Index of Biotic Integrity, habitat quality, and channel stability.  Channel stability has long been considered integral for maintaining healthy biotic communities and habitat quality, although empirical evidence of these relationships is limited.  Physical indicators of channel condition may be useful in determining biotic impairment for non-point dominant TMDL problem investigations.  In summer 2005, we analyzed fish communities (IBI), habitat quality (a modified Qualitative Habitat Evaluation Index; QHEI), and channel condition (Pfankuch’s Stream Reach Inventory and Channel Stability Evaluation).  We found a significant positive correlation between IBI and channel stability using Inverse Pfankuch score in the Snake River Basin in eastern Minnesota (r_s = 0.53, p = 0.05, n=14), whereas results were not significant in the Redwood River Basin in southwestern Minnesota (r_s = 0.10, p = 0.27, n = 14).  We found a significant positive association between IBI and QHEI scores for the Redwood River Basin (r_s = 0.64, p = 0.01; n=14), whereas results were not significant in the Snake River Basin (r_s = 0.25, p = 0.41, n = 13).  Finally, an analysis of Inverse Pfankuch scores with QHEI scores was not significant for either basin (Snake River Basin:  r_s = 0.20, p = 0.50, n = 13; Redwood River Basin:  r_s = 0.16, p = 0.59, n = 14).  Although our results do not demonstrate a significant association between channel stability and habitat quality, we recommend that both habitat and channel condition assessments should be used together to identify potential causes of biotic impairment.