All rivers and canals conveying water contain eroded sediments. Increase of soil erosion due to Catchment degradation especially in developing countries has resulted into increased siltation Problems in rivers and canals. To successes the small-scale irrigation managing the sediment and irrigation periods are very important rolls. Ethiopia was constructed plenty of small scale irrigation projects to decrease the poverty .But in most of the irrigation canal there is a serious sedimentation problems due to soil erosion and poor management of erosion protection. .The study implemented in around 2000m long masonry rectangular canal in Bebeks small Schell l irrigation project. And it irrigated around 30ha command area from spring water source. Even if the released water free from silt, the canal faced silted during non-irrigation period due to the incoming of sediment from the upstream watershed around 60ha area. During analysis of the model, calibrating of HEC_RAS where done for more sensitive parts manning’s roughness and gate 0.0185 values. In case of validation proses, using the calibrated values of manning’s roughness the coefficient of regression R2 values become 0.6926. And other model SWAT also used for the predicting of total sediment transport from the watershed and the result also gate 8 ton/ha values obtained. And used this value as input of HEC_RAS sediment interring load. Other important parameter to select appropriate sediment transport method is median sediment grade. And obtained from sieve analysis 1.056mm. During the sediment transport rate analysis the model indicates erosion and deposition occurrence. The model run in three scenario based on different load assumption. In scenario one the model run with 10% total incoming load from the watershed and it shows erosion and deposition occurrence. High deposition showed in cross section 22 and 7 (0.240, 0.519ton/year) respectively. And also in scenario two the model run by applying 20% sediment load .in this also there is erosion and deposition with same variation of deposition shows in cross section 22 and 7 with a value of (0.332, 0.426 ton/year) respectively. The third scenario running the model using 30% of sediment load, and also shows deposition and erosion occurred in cross section 22 and 7 (0.274, 0.614 ton/year) respectively.