In an effort to make irrigation schemes more flexible, efficient and reliable, the number of flow control structures has sharply increased during the modernization and development of the schemes. But this makes the flow non-uniform and can cause sedimentation problems. The Sunsari Morang Irrigation Scheme (SMIS) in Nepal is being modernized and sediment management is one of the major issues in the design. The sediment transport model SETRIC was used to analyse canal operation and flow control on one of the modernized secondary canals (S9). Suggested operation and control in the design was not followed during the irrigation season. The simulation showed that the potential improvements just in canal operation would result in reduced sediment deposition.