Additional and refurbished pumping stations are required to mitigate the intensifying occurrence of droughts and floodings. These installations negatively impact threatened freshwater fish populations due to the increased risk of injury and mortality when fish pass through them. Fish-friendly pumping installations have been proposed as a potential solution to reduce these risks. However, published assessments of these new types of pumps remains lacking, and the few available studies do not enable a cross-comparison with conventional pump types. The promising, yet understudied, Fairbank Nijhuis ‘fish-friendly’ axial flow pump has been assessed in previous works, however the results remain ambiguous due to low recapture rates, unconsidered parameters, fixed operating conditions, and the inability to identify the likely sources of injury and mortality. In this study, we address the limitations of previous works by implementing a standardized protocol for live fish in conjunction with passive barotrauma detection sensors. The major finding of this work is that safe passage of eel (100% survival) is confirmed, but that bream and roach had a much lower survival probability (24% and 70% survival respectively) than expected, albeit higher than for a conventional axial flow pump (roach survival: 13%). Furthermore, roach and bream passing at higher rpm suffered significantly higher mortalities. The impact of the impeller was found to be the most common source of severe injury for both pumps. These results are significant because they conclusively show that fish-friendly pumps may be considered safe for eel, but not for other endemic European fish species such as roach and bream.