AbstractIrrigation systems performance and sustainability are affected by sediment deposition. Cohesive sediment (suspended load) is an important problem in irrigation canals and its behaviour is significantly different from that of non‐cohesive sediment (bed load). Most studies on sedimentation in irrigation systems deal with non‐cohesive sediment. Studies on cohesive sediments are mostly done in rivers and estuaries, but not in irrigation canals. The few existing studies on cohesive sediment in irrigation canals are limited by their use of 1D models. Therefore, in this study we test whether an existing 3D model that was designed for rivers and estuaries can be used in irrigation canals. Delft3D was identified as a suitable model. Simulations were done for different sizes and configurations of the irrigation network. After some adaptations to the model, the simulations of different scenarios provided promising results. From a hydrodynamic and morphological point of view the Delft3D model was able to realistically represent water and sediment flows in a hypothetical canal set‐up, consisting of a main canal, a branch canal and several hydraulic structures. Some challenges remain in the use of Delft3D for irrigation canals, in particular regarding wall roughness in small rectangular canals and computation times for complex systems. However, these challenges are not insurmountable and the advantages of using Delft3D are clearly shown in this paper. © 2019 John Wiley & Sons, Ltd.