The European Union Marine Strategy Framework Directive (MSFD) includes four descriptors of Good Environmental Status (GES) which are affected by fishing activity. These descriptors are: biodiversity, fish stocks, foodweb, and seabed integrity. This paper shows how these descriptors can be related to variables within an ecological model and how an ecological model can be used to analyse whether the fishing pressure that is estimated based on bioeconomic criteria is within general sustainable limits. The paper presents an example of such an analysis of the Eastern Baltic cod fishery using two models: a bioeconomic model and an ecological model. The models are calibrated based on historic data. The mapping between the descriptors specified by MSFD and variables available for analysis in the models is incomplete, e.g. genetics and spatial structures are not included in the models. The models can be used strategically, providing a qualitative understanding of the anticipated relative changes.