The use of renewable energies including hydropower energy is growing throughout the world. Among the existing hydropower technologies, small-scale hydropower technologies are popular due to easy accessibility and availability in different locations. Recently, Archimedes Screw Turbines (ASTs) as a new technology have been considered. The main objective of this research is the structural optimization of an AST for substituting in irrigation canals instead of existing check structures. For this purpose, the AST performance model was numerically developed for screw performance optimization in MATLAB 2013a environment. The developed model was validated using experimental data. Different structural parameters were optimized to design an appropriate AST for replacing instead of check drop-1 in the east Aghili canal in Khuzestan province (Iran). The canal was simulated using the ICSS hydrodynamic model. The results of the developed model showed a good agreement with reported experimental data. The highest efficiency was obtained 90.83% for the screw length of 6 m, the inclination angle of 20°, and the flight number of 1 at the design flow rate. Based on the findings, the suggested system can be used instead of the canal structures without considerable change in the hydraulic and performance of the canal.