The first major collection of freshwater fishes was made by Dr Rex Jubb in 1931. He and his wife worked at the Museum between 1959 and 1980 and they produced the first book on the freshwater fishes of southern Africa. Today the Department houses important historical collections of southern African freshwater fishes. The collections incorporate the holdings of the Natal Museum (dating back to 1905) and the South African Museum (dating back to 1875); consequently the coverage of the Eastern and Western Cape and Kwazulu-Natal fish is expecially good.

The collection comprises 14 200 accessions which total some 250 000 specimens, mostly stored in alcohol. The entire database is computerised and is regularly accessed by national and international scientists as well as by nature conservation officials and consultants. The Albany Museum maintains a close association with the Department of Ichthyology at Rhodes University, the Institute for Water Research and the South African Institute for Aquatic Biodiversity (formerly the JLB Smith Institute of African Ichthyology), making the collection of freshwater fish species in this department important in the study of a number of related research fields.