The Unazuki Reservoir is located on the Kurobe River, which is influenced by a catchment with one of the highest sediment yields in Japan. Due to a sufficiently available discharge during flood events, annual sediment flushing with full water-level drawdown (i.e., free-flow sediment flushing) is conducted to preserve the effective storage capacity of the reservoir. Nevertheless, the upstream half of the reservoir (i.e., study segment) suffers from the excessive deposition of coarser sediments. Remobilization of these coarser materials and their transportation further downstream of the reservoir is a priority of reservoir owners for sustainable reservoir functions, such as flood-risk management and hydroelectric energy generation. In this paper, an already conducted sediment-flushing operation in the Unazuki Reservoir is simulated, and its effects on sediment scouring from the study segment of the reservoir together with changes in bed morphodynamics are presented. A fully 3D numerical model using the finite volume approach in combination with a wetting/drying algorithm was utilized to reproduce the hydrodynamics and bed changes using the available onsite data. Afterwards, the effects of discharge adjustment on the morphological bed changes and flushing efficiency were analysed in the study segment using an additional single-discharge pulse supplied from upstream reservoirs. Simulation results showed that an approximately 75% increase in the average discharge during the free-flow stage changed the dominant morphological process from deposition into an erosive mode in the study segment. If the increase in discharge reaches up to 100%, the flushed volume of sediments from the target segment can increase 2.9 times compared with the initiation of the erosive mode.