Rising floodwaters in the Blue Nile (BN) and White Nile (WN) tributaries continually affects people’s lives and the safety of infrastructures in Khartoum, the capital of Sudan. Recently, floods have covered a wide area of Khartoum and destroyed many buildings and bridges. We conducted this study to evaluate and predict the flood effects around BN and WN in Khartoum to make recommendations in view of upcoming flood disasters. Land-use/land-cover (LULC) changes after floods that occurred in 2014, 2016, and 2020 were evaluated and LULC was predicted for 2024 by applying a combination of remote sensing (RS) and geographic information-system (GIS) techniques. We also evaluated the expected hazard due to floods. Our results showed that the agricultural, built-up, and water changes around BN were 0.30%, 0.25%, and 0.05%, respectively, for the period 2014–2016, and, that changes for the period 2016–2020 were 3.38%, 3.68%, and 7.28%, respectively. Correspondingly, the agricultural, built-up, and water changes around WN were 5.56%, 3.26%, and 8.02% during 2014–2016 and 13.79%, 5.62%, and 21.40% during 2016–2020. The change estimation indicates that the most flood effects in the region occurred around WN, possibly covering the whole areal extent of Khartoum city. The area covered by waterbodies may decrease by 4.18% (BN) and 20.35% (WN) during 2020–2024, based on RS–GIS evaluation, but hydraulic evaluation shows that the expected hazard due to floods in Khartoum is high. Thus, flood-risk assessments should take into account both physical hazard and the distribution of the population across the whole area of Khartoum.