Abstract In early 2003 a series of large, wildfire-related sediment slugs occurred in streams in the south-eastern Australian alpine region. Back-pack and boat-mounted electrofishing were used to measure changes in riverine fish fauna after one particularly large sediment slug which started in an upland stream and then travelled downstream through 200 km of third and fourth order stream. Twelve impact sites and eight control sites were surveyed where there were previous data on fish populations. The sites were surveyed directly after the sediment slug had passed and then 12, 24 and 36 months after. Immediately after the sediment slug, fish abundances fell by between 95–100% at four impact sites in the upper reaches of the study area, primarily due to the effect of low-dissolved oxygen levels. Twelve months later fish numbers were still decreased in the upper catchment but showed signs of recovery after 24 months. Further downstream, where water quality was not as severely affected by the sediment slug, the effects on native fishes were less apparent. The circumstances of these events represented a unique opportunity to obtain baseline data regarding the effects of post-fire disturbances on fish, and their time to recovery. If fire were to occur in catchments where endangered species exist, our results suggest that actions such as translocation may be required to ensure the long-term survival of threatened species.