Between 1950 and 1970 the National Institute for Water Research (NIWR) of the Council for Scientific and Industrial Research undertook a number of surveys of many South African Rivers. As a result, a large collection of material was identified by local and overseas scientists. The Director of the Museum, Dr Jacot-Guillarmod, offered to accommodate these collections and they were transferred to the Museum in 1972. This material, together with existing collections and the donation of the Omer-Cooper collections of aquatic beetles, formed the National Collection of Freshwater Organisms. The Algal and Diatom collections were retained by the CSIR and hence the collection is more correctly named the National Collection of Freshwater Invertebrates.
The collection currently holds in excess of 1.5 million specimens including over 1000 primary and secondary types. These are being added to through an active programme of research as well as donations and voucher specimens from river surveys. Information on more than 120 000 accessions is available in hand written catalogues and a computer database. All groups of aquatic invertebrates, from the entire Afrotropical Region, are represented in the collection, although active research and growth is largely restricted to the African continent, focussing mainly on southern Africa.