The Stockholm University Baltic Sea Centre was established 1 January 2013, and is a merger of two organizations, the previous Stockholm University Marine Research Centre and the international research collaboration Baltic Nest Institute.

Baltic Eye was formed in 2013 when the foundation BalticSea2020 ventured a strategic partnership together with Stockholm university and its Baltic Sea Centre.

Administration of the strategic marine environmental research programme: Baltic Ecosystem Adaptive Management, BEAM, was part of the Baltic Sea Centre up until 2015.

Management and locales
The Centre is managed by the Centre director; Tina Elfwing, the scientific supervisor; Christoph Humborg and BNI's director; Bo Gustafsson.

A board consisting of members from the University as well as external representatives will approve and influence activity plans and guide the strategic direction of the Centre.

The Baltic Nest Institute, BNI, remains as an identifiable unit and maintains its international board.

The Stockholm University Marine Research Centre has ceased as of this decision by the university management, but all activities and resources, including the Askö Laboratory, continue as part of the new Baltic Sea Centre.