Abstract The total number and condition of fish extracted via high and low flow irrigation pumps was assessed over a 2-year period in the Namoi River, Australia. A combination of boat electric fishing and fyke netting was used for 10 weeks during the peak irrigation period to determine species and size classes susceptible to entrainment during water abstraction. Over 2300 fish passed through the pump outlets over the study period, with many individuals (7.5% of total) both killed and injured. The maximum number of fish entrained in a single day was 232. Mortality was significantly higher from the high volume pump site, but only large (>200 mm long) or small (<50 mm long) fish were killed. Medium-sized fish (50–200 mm long) largely survived the abstraction process; although 70 were injured (3% of total), only one was killed (0.07%). The Electric fishing surveys showed that only four species were present in storage dams, suggesting that survival through the pump systems may be size and species specific. Fish that survived the water abstraction process had no opportunities to return to the main river system and were effectively classified as lost from the main river population. The development of suitable mitigation measures, including operational changes and screening, are suggested as mechanisms to prevent extraction and minimise any adverse impacts arising from irrigation development.