The impacts of fisheries on ocean resources are no longer considered in isolation but should account for broader ecosystem effects. However, ongoing ecosystem-wide changes added to the inherent dynamics of marine ecosystems, create challenges for fisheries and fisheries management by affecting our ability to ensure future fishing opportunities and sustainable use of the seas. By reviewing a corpus of fisheries science literature, we contribute to informing managers and policymakers with considerations of the various threats to fisheries and the marine ecosystems that support them. We identify and describe 25 ecosystem challenges and 7 prominent families of management options to address them. We capture the challenges acting within three broad categories: (i) fishing impacts on the marine environments and future fishing opportunities, (ii) effects of environmental conditions on fish and fishing opportunities, and (iii) effects of context in terms of socioeconomics, fisheries management, and institutional set-up on fisheries. Our review shows that, while most EU fisheries are facing a similar array of challenges, some of them are specific to regions or individual fisheries. This is reflected in selected regional cases taking different perspectives to exemplify the challenges along with fishery-specific cases. These cases include the dramatic situation of the Baltic Sea cod, facing an array of cumulative pressures, the multiple and moving ecosystem interactions that rely on the North Sea forage fish facing climate change, the interaction of fishing and fish stocks in a fluctuating mixed fishery in the Celtic Sea, the bycatch of marine mammals and seabirds and habitat degradation in the Bay of Biscay, and finally the under capacity and lack of fundamental knowledge on some features of the EU Outermost Regions. In addition to these ecoregion specific findings, we discuss the outcomes of our review across the whole of European waters and we conclude by recognizing that there are knowledge gaps regarding the direction of causality, nonlinear responses, and confounding effects. All of the challenges we identify and characterize may guide further data collection and research coordination to improve our fundamental understanding of the system and to monitor real changes within it, both of which are required to inform an Ecosystem Approach to Fisheries Management (EAFM). An European EAFM could build upon an array of management measures currently tailored for fisheries management only, including promoting funding interdisciplinary research and ecosystem monitoring. Such integrative management should reduce uncertainties in environmental, social and economic trends, and lower the risk for disruptive events or ecosystem effects with far-reaching consequences, including a shift toward less productive marine ecosystems.