Initially CFFR was the Canadian Committee on Freshwater Fisheries Research and was formed to take over some of the functions of the National committee on Fish Culture which was a joint committee of the National Research Council and the Biological Board of Canada (renamed the Fisheries Research Board of Canada in 1938). The first meeting of the CCFFR, sponsored by NRC, was held in Ottawa on January 6, 1948, and its terms of reference stated that the CCFFR "act as a clearing house for information and as a forum for discussion of common problems, to promote the coordination of research and technique, to consider what researches ought to be undertaken and to recommend accordingly, to give advice on the granting of funds for specific researches when such advice is requested and to advise on the dissemination of information". Initially it was a forum where research proposed by government scientists was reviewed by Canada’s academic community. CCFFR evolved from a committee into an organization that was wholly dependent on government financing to a self financed organization whose sole purpose was to convene one conference a year on a cycle of East-Centre-West-Centre. CCFFR was incorporated in 2009 to protect local arrangements Chairs from personal liability and the founding CCFFR Board was specific in deciding that the organization existed to convene the conference and it had no policies or procedures and took no positions on behalf of its members.

The Society of Canadian Limnologists (SCL) came to life during the 1975 meeting of SIL at the Freshwater Institute in Winnipeg, responding to a broadly held perception that Canada’s freshwater scientists must find better ways to communicate with one another and speak with a common voice. The earliest presidents of SCL included Marcel Ouellet (1979–1981), and Michael Dickman (1981–1984) at Brock University. SCL initially evolved from SIL-Canada which existed under the directorship of Fred Ward at the University of Manitoba and Diane Malley at the Freshwater Institute. SCL first participated in a joint national conference in partnership with the Canadian Conference for Fisheries Research in 1979, and has participated in annual meetings with CCFFR every year since then. In 2014, the SCL held a joint meeting for the Genomes to Biome conference, co-organized with the Canadian Society of Ecology and Evolution (CSEE) and the Canadian Society of Zoologists (CSZ). SCL began recognizing lifetime achievement in Limnology with its Rigler Award starting in 1985, and student achievement started being recognized with the Peters Award starting in 2007. In 2018, the SCL was federally incorporated as a not-for-profit organization and several members of its first Board of Directors played an active role in the creation of SCAS.