Qualitative stream habitat indices are important tools in classifying, interpreting, and assessing the conditions of stream ecosystems. Habitat indices are numerical values produced from scoring various features of a stream. Three commonly used habitat indices are the qualitative habitat evaluation index (QHEI), the rapid bioassessment protocols (RBP), and the riparian, channel, and environmental inventory (RCE). All three indices were used to assess the habitat conditions of 18 prairie streams of different sizes and environmental settings in the Red River of the North basin. Correlations suggest that these three indices provide similar results (r ranged from 0.83 to 0.85, P ≤ 0.003); however, the indices emphasize different aspects of the stream environment. Metrics from each index were classified as one of the following: channel geomorphology, riparian zone, substrate related, and instream cover and biota. The QHEI and RBP indices emphasize channel geomorphology metrics (41% of total score for the QHEI and 42% of the total score for the RBP). The RCE had a more balanced emphasis among the four classes but emphasized riparianzone metrics (32% of total score). There is redundancy within indices. Several metrics showed high correlations (e.g., r = 0.74 for land use and riparian-zone width in QHEI; r = 0.86 for bank vegetative protection and bank condition in RBP; r = 0.83 for macrobenthos and fish in RCE). To evaluate biological applicability, index scores were correlated to scores of the index of biotic integrity and fish community statistics of species richness, evenness, diversity, and percent of individuals in four trophic groups. No significant correlations were identified. We concluded that the metrics making up the habitat indices were either not applicable or not weighted appropriately for northern prairie streams.