We assessed the biotic integrity of the middle-to-upper Delaware River. We sampled fish and assembled water quality data for eight stations and three habitat types (pool, riffle, and submerged aquatic vegetation [SAV]) of the Delaware River and applied an existing index of biotic integrity (IBI) recently developed for the northern mid-Atlantic slope drainages. We used Spearman's correlation to test IBI scores against measures of water quality (WQI) and cultural pollution. IBI scores were not significantly correlated with WQI, but were significantly negatively correlated with sewage load of adjacent tributaries (r_s = −0.647, p = 0.08). Sites ranged from good to fair in biotic integrity. Fish assemblage composition from all three habitat types was necessary in order to accurately characterize biotic integrity. Of the three habitat types, fish assemblages from SAV habitats had the greatest positive effect on biotic integrity. Continued application of the IBI may be useful as a long-term monitoring tool as this river corridor becomes increasingly urbanized.