The objective of this study was to determine the relationship between fish assemblage and habitat in streams dominated by an agricultural landscape. Fishes from 20 natural and 20 channelized streams were sampled using electrofishing gear in east central Indiana. Streams that had been channelized had a lower quality fish assemblage when compared to natural streams as measured by the Indiana V. Eastern Corn Belt Plain Index of Biotic Integrity (IBI). Stream habitat was evaluated using the Ohio EPA Qualitative Habitat Evaluation Index (QHEI), which indicated that channelized streams had lower quality primarily due to a loss of heterogeneous habitat. Pearson correlation analysis relating IBI and QHEI was positive and significant and demonstrated that a reduction in riffle and pool areas associated with channelization was the most significant factor influencing the fish assemblage. Furthermore, species lost when streams were channelized were predictable and often represented environmentally sensitive species. The results of this study suggested that stream channelization has a negative influence on the fish assemblage which should be recognized before any stream development.