Food webs are central entities mediating processes and external pressures in marine ecosystems. They are essential to understand and predict ecosystem dynamics and provision of ecosystem services. Paradoxically, utilization of food web knowledge in marine environmental conservation and resource management is limited. To better understand the use of knowledge and barriers to incorporation in management, we assess its application related to the management of eutrophication, chemical contamination, fish stocks, and non-indigenous species. We focus on the Baltic, a severely impacted, but also intensely studied and actively managed semi-enclosed sea. Our assessment shows food web processes playing a central role in all four areas, but application varies strongly, from formalized integration in management decisions, to support in selecting indicators and setting threshold values, to informal knowledge explaining ecosystem dynamics and management performance. Barriers for integration are complexity of involved ecological processes and that management frameworks are not designed to handle such information. We provide a categorization of the multi-faceted uses of food web knowledge and benefits of future incorporation in management, especially moving towards ecosystem-based approaches as guiding principle in present marine policies and directives. We close with perspectives on research needs to support this move considering global and regional change.