For the past few years, the sediment began to accumulate in Al-Gharraf River which reduces the flow capacity of the River. In the present research, a numerical model was developed using Hec-Ras software, version 5.0.4. to simulate the flow and sediment transport in the upper reach of the river. The hydrological and cross-section data measured by the Ministry of Water Resources, for the reach located between Kut and Hai cities and having a length of 58200 m, was used to perform calibration and verification of the model. Moreover, field sampling of suspended and bed loads was gathered for five months starting from 7/2/2019, and laboratory tests of samples were conducted to be used as input data in the model. Actual flowrates for the year 2018 were used to predict the sediment accumulation in the river, and the results show that the accumulated deposition was ranged between 2.5 cm to 1m, while the erosion depth ranged between -4cm to -2cm. Furthermore, the estimated amounts of sediment discharges were ranged between 70 and 1308 Tones/day. Then four scenarios of flowrates ranged between 100-300 m3/s were used to analyze the possible sedimentation problems and to propose the treatment needed to preserve the morphology of the river The results show that the invert changes of bed depth were ranged between -2 to 9 cm, and the sediment discharge ranged between, 33 to 970 Tones/day. A lining of specified sub-reaches using the concrete or by the grouted riprap was proposed to avoid sedimentation or erosion respectively.