The present research discusses a problem of seal damages in dam gates due to influence of water flow through sluices passage way. The low level sluices (L.L.S) of Merowe dam were taken as a research field to investigate the influence of flow on the gate seal. The core of the problem is that the rubbery seal of L.L.S gates is damaged and washed out during yearly operation in flooding season. In previous years there is many solutions has been tried in two ways: first way is by improvement of seal fixture, and the second way is the hydrodynamic approach which focusing on flow behavior in the areas close to the seal. The present study is going through the second approach and a computational fluid dynamic (CFD) software was used to build a model and simulate the water flow through sluice passageway. One of the main result obtained from the study is that the high shear force – as a result of high flow velocity and pressure - subjected on the lower seal is the main cause of the seal damage and it can be reduced by small change in the geometry of that area. The software model results was validated by comparing against instruments measured values and physical observations in the damages area, then finally the research results was concluded and recommendations was introduced.