Sediments cause serious problems in irrigation systems, adversely affecting canal performance, driving up maintenance costs and, in extreme cases, threatening system sustainability. Multiple studies were done on the deposition of non-cohesive sediment and implications for canal design, the use of canal operation in handling sedimentation problems is relatively under-studied, particularly for cohesive sediments. In this manuscript, several scenarios regarding weirs and gate operation were tested, using the Delft3D model, applied to a case study from the Gezira scheme in Sudan. Findings show that weirs play a modest role in sedimentation patterns, where their location influences their effectiveness. On the contrary, gate operation plays a significant role in sedimentation patterns. Reduced gate openings may cause canal blockage while intermittently fully opening and closing of gates can reduce sediment deposition in the canal by 54% even under conditions of heavy sediment load. Proper location of weirs and proper adjusting of the branch canal's gate can substantially reduce sedimentation problems while ensuring sufficient water delivery to crops. The use of 2D/3D models provides useful insights into spatial and temporal patterns of deposition and erosion but has challenges related to running time imposing a rather coarse modelling resolution to keep running times acceptable.the sediment transport which leads to sediment deposition and erosion in different locations of the canal. Even though canals are typically designed to keep the bed free from sediments and convey sediments to fields, the improper placement and operation of gates and weirs in the absence of optimal canal operation plans may lead to deposition and erosion of sediment in canals and reduce canal performance. The impact of canal operation on sedimentation problems in irrigation systems deserves more attention in modelling studies of irrigation systems.Examples of studies simulating the effect of canal operation on sediment transport include Reference [8] in the Sunsari Morang system in Nepal and Reference [9] in the Machai Maira Branch Canals in Pakistan. However, both studies only considered non-cohesive sediment, mostly transported as bed material. In reality, many irrigation systems deal with a mix of coarse (non-cohesive) and fine (cohesive) sediment. Dealing with sedimentation in irrigation canals becomes more complex in case of cohesive sediments due to its physiochemical properties and inter-particle forces. Most studies regarding cohesive sediment behavior have been done in rivers and estuaries [10][11][12][13][14][15]. There is a great need to study the mechanism of cohesive sediment transport in irrigation canals [16], in particular under different scenarios of gate operation.The impact of gate operation on the cohesive sediment in the Gezira Scheme in Sudan has been studied by Reference [17]. They considered two gate operation scenarios: (1) a system in which water allocation is based on water duty and the cropped area and water is given b...