The objectives of this study were to evaluate fish guild compositions and national river health using a multi-metric model of the Korean index of biological integrity using fishes (K-IBIF) in four major Korean watersheds along with water chemistry and habitat quality. Tolerant and omnivore fish species dominated all the watersheds, and the proportions of tolerance guilds and trophic guilds reflected water chemistry and habitat quality. The number of sensitive species and insectivore species had negative correlations (r < −0.42, P < 0.01) with chemical water quality (biological oxygen demand (BOD)), while tolerant species and omnivore species had positive correlation (r > 0.27, P < 0.05) with BOD values. Physical habit conditions, based on qualitative habitat evaluation index (QHEI) model, indicated a “good” condition (mean = 68.9; range = 45–105) in three watersheds, except for the Yeongsan River watershed. Values of QHEI were significantly correlated (R2 > 0.4, P < 0.01) with nitrogen and phosphorus levels in all watersheds, suggesting that habitat degradation is associated with eutrophication. Model values of K-IBIF in the watersheds averaged 18.2, indicating a “fair” condition, and about 37% of all observations in K-IBIF model values were judged as a “poor” health condition, indicating severe health impairment. Overall, our data suggest that degradation of the river health was due to a combined effect of chemical pollution and physical habitat modifications. This research provides valuable information on Korean river conservation and restoration in the future.