Reservoir sedimentation is known to be a key issue worldwide. One operational measure to deal with sediment accumulations is flushing; however, efficiency is often lacking. The goal of this study is thus to improve the effectiveness and efficiency of flushing operations in short, mountainous reservoirs used for peaking hydropower generation by introducing guide walls into the system. To do so, two purely theoretical topographies with systematically placed guide walls were analysed. The different configurations were compared based on three performance indicators: ratio of evacuated over inflow sediment, as well as local and global bed shear stresses. It was found that even small changes in location and flow alignment of the guide walls may significantly change flow patterns inside the reservoir. In a last step, the methodology was applied to a case study, the Jiji hydropower plant in Burundi, presently under construction, and whose live storage will be paramount to regulate the power network in the country on a daily basis.