Freshwater fishes are regarded as South Africa’s most threatened species group. Long-term distributional data for freshwater fish species can be vital for detecting critical ecosystem changes, such as species range shifts, new records of non-native invasions and loss of ecosystem services or unique biodiversity. Understanding exactly how the abundance and distribution of freshwater fishes (both native and non-native) are changing is pivotal to effectively manage and conserve unique and threatened freshwater biodiversity and ecosystems. In light of this, a comprehensive freshwater fish dataset (freshwaterbiodiversity.org) was built, comprising all available records of formally described freshwater fish species occurring in South Africa. The comprehensive search for data resulted in the accrual of a total of 60 837 records of freshwater fish from South Africa, which includes 35 955 records new records to the Global Biodiversity Information Facility (GBIF). Of the 101 native species occurring in the country, almost half of all assessed species were found to be threatened, with the number of occurrences decreasing in recent years. Conversely, the number of occurrences and distribution ranges of many non-native species were found to be increasing, especially within the past three decades. These data have provided a much-needed update to the known status and distribution of freshwater fishes in the country.