The Bavarian Danube River has experienced numerous large flood events in recent years which make flood management an urgent matter. The propagation of flood waves along the river is heavily influenced by controlled and natural flood retention. Over the past centuries, natural flood retention areas were lost due to river training, and the hydraulic characteristics of the channel-flood plain system were modified. The purpose of this paper is to understand the effect of river training on the flood retention characteristics along the Bavarian Danube. Systematic two-dimensional hydrodynamic modelling shows that extreme floods are attenuated more strongly in the present state of the channel-flood plain system than they were historically. This is because the retention areas are filled later during the event, so the attenuation effect is much larger for the same magnitude of the retention volume. Natural flood retention is therefore not an effective management option for reducing extreme floods on the Bavarian Danube. Controlled flood retention measures provide a higher efficiency regarding peak attenuation to retention volume ratio. On the other hand, the delay of flood peaks due to natural retention may be beneficial for the superposition of the flood waves with contributions from downstream tributaries.