Lake Nubia (LN) is the upstream part of Aswan High Dam Lake (AHDL) that lies in Sudan. This portion has been well studied; however, its bed profile had been lacking due to the lake's complex morphology. The goals of this paper are to create a 3D model robust enough to capture the lake bed heterogeneity, conduct sensitivity data processing to increase confidence in created 3D profile, and provide engineering applications of this model to aid in the management of the lake. One of these applications involved in this study is to estimate the total amount of sediments deposited in LN in order to make it possible to optimize the utilization of the sediment and accurately manage its removal in a better way. In this study, the hydrographic survey data of the lake which is conducted by using the echo-sounder via field missions and remote sensing data represented in several Landsat ETM+ images are processed and analysed by Remote Sensing and GIS software to build the 3D profiles of the lake. The method used by the Aswan High Dam Authority (AHDA) based on the complementary cross-sections is evaluated too, and its results of the accumulated sediment amount in the lake are compared with the present one that is relaying on the created 3D profiles of the lake. The results showed that the total amount of sediment in the study area till 2012 is about 5.876 billion m3. Also, results indicate that the present approach overestimates the sedimentation amount by about 0.22% compared to the results of the method used by AHDA. In conclusion, the created 3D model using RS/GIS captured the heterogeneity of the lake efficiently. Consequently, this model was able to analyse this morphologically complex lake.