Irrigation canals play an important role in the economic development of Uzbekistan which is located in arid zone and shared user of transboundary water resources. Almost 75% of the irrigation network in Uzbekistan is unlined that subject to some natural processes such as vegetation, erosion, sedimentation, and seepage. The efficiency of the irrigation networks in Uzbekistan is about 63%. Lining of canals is the major protection measure against water scarcity for Uzbekistan. This study aims to investigate how the hydraulic properties of different lining materials such as geomembrane, concrete, asphalt, sand mixed bentonite and stone pitching affect the rehabilitation cost of canals. In this study, field data and hydrodynamic model HEC-RAC are applied for analyzing the use of different lining materials on the efficiency of the canal and then the costs of rehabilitation were compared. To apply the hydrodynamic model HEC-RAS, the flow and bathymetric parameters were measured by employing the acoustic Doppler current profiler system for a reach of length 1.0 km in the Tashkent magistral canal. The obtained R2 between modeled and measured data equals to 0.86. The use of different lining materials such as geomembrane, concrete, asphalt, sand mixed bentonite and stone pitching affect the channel geometry with different ranges from 21.69 to 34.41 per running meter (RMT). With different cross-sectional values, rehabilitation of the first reach of Toshkent magistral canal costs about $ 260, 688, 536, 286, 210 thousand respectively. For the point of lifetime, geomembrane then concrete, and stone pitching showed the minimum annual coverage value of $ 32, 46, 10 thousand per year, respectively. Stone pitching with the longest durability is the most efficient technique to improve water-use efficiency of Toshkent magistral canal. This study could help the policy makers to select the best material for lining based on the lifetime, cost and durability. Moreover, the efficiency of the irrigation networks will increase that play important role in water resources management.