Aquatic ecosystem management is considered a “wicked problem” for three reasons. These ecosystems are characterized by complex, time-varying interactions among species and their environment. Many large aquatic ecosystems are managed for multiple ecosystem services (e.g., fisheries, recreation, water quality) that cannot be simultaneously maximized. Finally, these systems continuously change due to natural cycles (e.g., El Niño) as well as human-driven environmental change (e.g., climate change, invasive species, nutrient pollution). For example, Lake Erie is a highly managed, dynamic ecosystem that has undergone significant changes since human settlement including overabundance of harmful algae, fisheries collapse, and species extirpations and invasions. These changes altered connections among ecosystem components and services yielding complicated ecosystem networks and subsequently the pathways to realizing management objectives. To achieve management goals and address the wicked problem of quantifying dynamic linkages among ecosystem components, we use ecosystem-based fisheries management (EBFM), which is seldom used in freshwater systems. Toward EBFM, drivers of fisheries recruitment in Lake Erie have been quantified, but the linkages among ecosystem components and how these components respond to environmental change and management have been overlooked. Using fuzzy cognitive mapping, we developed a conceptual model of interactions among Lake Erie’s ecosystem components (e.g., prey, habitat, nutrients, fisheries, physical processes). We quantified linkage strengths among ecosystem components within Lake Erie using stakeholder and expert opinions. Using scenario testing, we semi-quantitatively describe how management actions (e.g., invasive species management, recreational and commercial harvest) and environmental change (e.g., climate change) affect ecosystem components and their linkages and tradeoffs among ecosystem responses and services as well as identify drivers of ecosystem change. This research helps elucidate connections among management actions and Lake Erie’s ecosystem components to understand the wicked problem and guide similar efforts in other dynamic, freshwater systems.