CIESM operations are coordinated and managed by the Director General and a small team of scientists and other professionals based at the Commission Headquarters in Monaco. Strategic planning is controlled by CIESM Central Board, which regroups representatives of the 23 Member States of the Commission and is currently chaired by H.S.H. Prince Albert II of Monaco.

The large spectrum of CIESM activities ultimately rests on the cooperation and voluntary contributions of hundreds of marine scientists distributed for the most part on the shores of the Mediteranean and Black Seas. They act within the fold of scientific committees and taskforces that are directed by an international mix of Committee Chairs and Heads of Programs of high-level standing.