The CAPAM receives funding for research efforts from the USA Federal and State government agencies (e.g., NOAA Fisheries), non-government organizations (e.g., natural resource conservation groups), private industry (fishing and fish processing companies), and interested public (individuals and non-profit forums). Research funds are obtained from both formal requests for proposals from prospective organizations, as well as direct contributions from concerned groups, vested parties, and responsible management entities interested in developing and maintaining sustainable marine resource animal populations worldwide.

The majority of support for the Good Practices in Stock Assessment Modeling Program comes from NOAA through the National Marine Fisheries Service Assessment Methods Working Group. Additional funding comes from the International Seafood Sustainability Foundation (ISSF). Support for the White Sea Bass Stock Assessment Program comes from the Pfleger Institute of Environmental Research (PIER).