Currently, the Eastern Baltic cod (EBC) is in continuing decline. Supporting management efforts to assist in its recovery will require a functional understanding of the dynamics of the EBC and the Baltic ecosystem. However, aquatic environments are challenging to research as they are elusive, encompass many scientific disciplines and are complex adaptive systems. This thesis explores how modelling and simulation methods can be applied and adapted to meet the specific needs of fisheries biologies’ current challenges regarding the EBC and potentially those of other stocks in similar situations.