Baltic Nest Institute (BNI) is an international research alliance between Stockholm University Baltic Sea Centre, The Swedish Agency for Marine and Water Management, Aarhus University and the Finnish Environment Institute (SYKE). BNI was established in 2007 to continue the research conducted in the international research programme MARE (1999-2006).

The Baltic Nest Institute is responsible for the Nest system, a decision support system aimed at facilitating adaptive management of environmental concern in the Baltic Sea. Nest can be used to calculate required actions needed to attain politically agreed targets for the Baltic Sea ecosystem. The main focus of the model is on eutrophication and the flows of nutrients from land to sea. 

Baltic Nest Institute Sweden participates in several national and international projects aiming to understand the environmental problems in the Baltic Sea and show the consequences of different courses of action using marine modelling. Some of these projects are presented below.