Thirteen of South Africa's national parks contain aquatic systems which support 63 indigenous and 11 alien freshwater fishes. Indigenous fishes include 43 species of the Zambezian faunal group (70% of the national total), eight Karroid (47%), five Cape (31%) and seven species of Marine origin (79%). Six represented Zambezian species, two Marine origin, and all of the Cape and Karroid species are endemic to South Africa. Only three threatened species naturally occur within national parks (Serranochromis meridianus, Barbus andrewi, Pseudobarbus afer) all of which are classified as Endangered. Two extralimital IUCN threatened species (Chetia brevis and Oreochromis macrochir) have been introduced. At least three of the five lineages of Galaxias zebratus and two of the four lineages of Pseudobarbus afer occur within national parks in the Cape region. Many fish populations within national parks remain threatened, particularly by hydraulic alterations, impoundment, and predation by alien fishes. There are few aquatic systems within national parks where one or more of these threats are not prominent, and these collectively support only half of the freshwater fish species occurring in all national parks. Proposed management actions include determination and implementation of Environmental Flow Reserves in stressed systems, management of existing alien fish populations and prevention of new establishments, and regular assessments of fish communities.