Sand dune encroachment towards water courses represents a severe problem. The fallen sand inside water course reduces its cross section and storage capacity, constitute a good environment for the growth of aquatic weed, effect on water quality, and consequently reduce the hydraulic efficiency. The reach of Nile River situated between High Aswan Dam and Aswan Reservoir is one of the most important reaches in the Nile River in Egypt, the Egyptian share of Nile water passes through this reach. Also the operation of Aswan reservoir hydraulic power stations depend mainly on its water levels and storage capacity. It is located inside the dray region where the wind is active, the land surface is dray, rain fall is rare, and vegetated areas are small. The reach is subjected to active sand dunes movements. Add to the severity of the problem; the low level of water course, and the huge source of moving sand in west desert. The study reach acts actually as sand trap to the moving sand. The aim of this research was to study the phenomena of sand encroachment towards the study reach, identifying the most critical reaches along it, estimating the rate of accumulation of falling sand inside water course, and establishing a protection system to minimize the effect of sand dune encroachment towards it.