Native freshwater fish of Australia have a diverse but largely undescribed endemic pathogen and parasite fauna. However, due to long-shared evolutionary histories and virulence/transmissibility trade-offs, effects of these endemic pathogens and parasites appear to be subtle: significant impacts are rarely observed and epizootics have not been recorded. In contrast, a number of alien pathogens and parasites are now established across southern Australia, causing manifestly harmful effects to native fish species and known or suspected epizootics in native fish populations. Undetected and/or undescribed alien viral pathogens are also suspected of being present. Alien pathogens and parasites were introduced to Australia with imports of live alien fish or their fertilised eggs. A review of the scientific and historical evidence indicates that they have had, and continue to have, greater impacts on native fish species than previously realised—especially for freshwater species. This review also documents a previously unknown, Murray-Darling-Basin-wide epizootic of Murray cod Maccullochella peelii in 1929–30, which may have contributed to strong declines in the related eastern freshwater cod Maccullochella ikei. A serious Chilodonella epizootic of M. peelii in 1982 is also examined. In addition, a possible role for alien viruses of the family Iridoviridae (Ranavirus and Megalocytivirus) in the general decline of the critically endangered silver perch Bidyanus bidyanus, and the rapid collapse of two specific native fish populations—upper Murrumbidgee River B. bidyanus and Shoalhaven River Macquarie perch Macquaria australasica—is suggested. It is argued that the severity of the impact of the virulent alien oomycete Saprolegnia parasitica, both historical and present day, has been underestimated. Finally, action is recommended against emerging new pathogen and parasite threats, and the extreme risk current alien fish importations pose in introducing them. These will further threaten already stressed native fish populations in southern Australia, particularly across the Murray-Darling Basin.