Pumping of water during floods from hinterland’s drainage systems into the main river poses a health risk to fishes. Herein, we investigated the effects of pump passages on fish health of four conventional and one ´fish-friendly´ pump at the Danube River in Germany. Conventional and ‘fish-friendly’ pump types caused external fish injuries leading to direct and delayed mortality. Immediate mortality and injury intensity increased with revolution per minute (rpm) and differed significantly between pump types. At the ´fish-friendly’ Pentair pump, higher numbers of injuries resulting from blind force (e.g. haemorrhages, scale loss and fin tears) were detected than at the conventional pumps potentially due to the differences in blade design. The Köster pump at low rpm proved to be similar ‘fish-friendly’ as the special-developed ‘fish-friendly’ Pentair pump due to the low amount of sucked-in fishes. As measures to reduce the damaging potential for fishes, the pumps should run on low rpm as often as possible. This lowers the collision risks with machinery parts and hence the mortality rate as well as suction effects, which can be caused by high rpm. After long periods of anergic state, pumps should generally run on low rpm before adapting to higher rates.