Context The Murray–Darling Basin – Australia’s largest river system – is heavily dominated by alien fish. Native fish species have suffered numerous localised extinctions and ∼47% are listed on federal and/or state threatened species lists. Aims This paper explores the hypothesis that alien fish and alien fish stockings can be the primary cause of decline and localised extinction of large-bodied native fish species, as opposed to habitat degradation and river regulation. The Lower Goodradigbee River, which is unregulated, in excellent instream health over the great majority of its course, and replete with high quality habitat, is utilised as a case study. Methods I investigated the hypothesis by synthesising historical records with contemporary scientific research and recent field observations. The role of alien fish species, particularly alien trout species (Oncorhynchus mykiss and Salmo trutta) and constant stockings of them, were closely examined. Results Data support the hypothesis that domination by alien trout species and their continual stocking have lead to historical declines and localised extinctions of large-bodied native fish species. Continued alien trout stockings, along with more recent invasions of alien carp (Cyprinus carpio) and alien redfin perch (Perca fluviatilis), are inhibiting native fish recovery. A suspected field sighting of the alien fish pathogen atypical Aeromonas salmonicida is reported, and the status of the declining native crayfish Murray cray (Euastacus armatus), and potential alien fish impacts upon them, are examined. Conclusions The impacts of alien fish and alien fish stocking in Australia require major re-evaluation and dedicated research. Implications It is strongly recommended that stocking of alien trout into the Lower Goodradigbee River for angling cease in order to conserve surviving native fish and Murray cray populations. Conservation stockings to effect a Murray cod (Maccullochella peelii) recovery in the Lower Goodradigbee River are warranted.