BNI is currently a formal collaboration between The Resilience Centre, University of Stockholm and National Environmental Research Institute (NERI), University of Aarhus. Partners include the Swedish Environmental Protection Agency, Danish Institute for Fisheries Research at the Technical University of Denmark, and four departments in NERI.

BNI is managed by an executive board representing the financing institutions and by a management board including the heads of the two departments (Fredrik Wulff and Bo Riemann). The daily work is managed by Frederik Wulff in Stockholm and by Jacob Carstensen in Roskilde.

Executive Board
The main financiers are members of the Executive Board and their mandate is to approve overall budgets, strategies and activity plans. The Board meets twice a year.

Management group
The head of the Management Group is appointed by the Executive Board for a period of two years. The Management group prepares the strategies, budgets and activity plans for the Executive Board. The Management Group meets regularly each year and moreover when needed.

Advisory Group
An international advisory group of scientists and users advices the Management group and the Executive Board. The Advisory group is appointed by the Executive Board. The advisory group meets at least once a year.

Annual meetings
Once a year relevant persons involved in Baltic Nest Institute meet for a joint seminar.