Natural channel designs often incorporate rigid instream structures to protect channel banks, provide grade control, promote flow deflection, or otherwise improve channel stability. The long term impact of rigid structures on natural stream processes is relatively unknown. The objective of this study was to use long term alluvial channel modeling to evaluate the effect of rigid structures on channel processes and assess current and future stream channel stability. The study was conducted on Oliver Run, a small stream in Pennsylvania relocated due to highway construction. Field data were collected for one year along the 107 m reach to characterize the stream and provide model input, calibration, and verification data. FLUVIAL-12 was used to evaluate the long term impacts of rigid structures on natural channel adjustment, overall channel stability, and changing form and processes. Based on a consideration of model limitations and results, it was concluded that the presence of rigid structures reduced channel width-to-depth ratios, minimized bed elevation changes due to long term aggradation and degradation, limited lateral channel migration, and increased the mean bed material particle size throughout the reach. Results also showed how alluvial channel modeling can be used to improve the stream restoration design effort.