The effects of agricultural drainage on aquatic ecosystems have been well documented. One of the primary impacts, particularly in floodplain habitats, is loss of river connectivity and associated fish passage. In the Lower Waikato River Basin in New Zealand, the loss of natural gravity fed flows caused by subsidence of peat has resulted in many ‘one way’ flood pumps. These pumps now operate against gravity to keep this lower elevation agricultural land free from flooding. Although fish mortality through pump-stations is known to occur, few studies have documented the degree of mortality and or trauma that occurs during typical operating scenarios. Nevertheless, it has been noted that when fish, particularly eels, are migrating through pumps that a distinctive sound is made by the pump as the blades strike them. In this investigation, and for the first time to our knowledge, we explore the potential to use hydrophones as a potentially cost effective remote monitoring (‘listening’) tool to assess eel mortality at a relatively common type of axial pumping station. We evaluated the range of sound and trauma experienced by both resident and released migrant eels passing through pumps during a typical autumn migration period. We also attempted to catalogue the ‘type’ range of sounds made by freshly euthanized eels and compared them to those of goldfish to illustrate differences. These type sounds are currently being used in the Waikato to develop pump and anguillid specific algorithms to evaluate the degree of mortality that may be occurring at other sites. It is envisioned that this approach will result in a range of information that has substantial potential to improve future management options and approaches at these and possibly other structures.