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Land drainage and flood-relief pumping stations are crucial infrastructure to safeguard lives, property, and agriculture from the devastating threat of flooding. However, these pumping stations create unwanted barriers to fish migration and can pose health risks, particularly for anguillid eels, which primarily live in freshwater but migrate to the ocean for reproduction. Fish-safe pumps have the potential to mitigate fish injury and mortality, but assessments of conditions during fish passage are lacking. This case study features a state-of-the-art full-scale live-fish pump testing facility, equipped with an axial-flow pump with a fish-safe design, to inform fish-focused pump design and optimize hydraulic conditions prior to live-fish testing. The potential for damage to passing fish was numerically investigated at optimal operating conditions using volume-based criteria, analyzing predictions from Computational Fluid Dynamics (CFD). Specifically, a damage index ( ξ ) was obtained for five hydraulic stressors that exceeded injury thresholds within rotating parts of the pumping equipment. In terms of hydrodynamic damage, the rate of pressure change ( d p / d t ; 3.2%) had the highest negative effect on fish, followed by damage caused by wall shear stress ( τ 0 ; 0.8%), and spatial velocity gradient ( d u / d y ; 0.07%), and thus should be minimized in future designs. The hydrodynamic damage due to rapid pressure changes (RPC) or low absolute pressure ( p abs ) within the impeller was negligible. Consequently, for the studied pump, the main priority should be optimizing rotor blade geometry while maintaining pumping efficiency, followed by reducing the risks of rapid pressure change and shear damage. Overall, this numerical assessment of the axial-flow pump provided invaluable insights into mechanisms of fish damage, informing future further improved designs without the ethical concerns and logistical challenges associated with live fish testing. • Eel passage conditions through a fish-safe axial-flow pump were assessed using a CFD model at the best efficiency point. • Several hydraulic stressors, relating to fish/eel damage, were numerically evaluated. • Predicted damage index values for each hydraulic stressor were in the range 0–0.032. • Rate of pressure change, ratio of pressure changes, and wall shear stress were the most dominant.