Marine ecosystems are complex, and there is increasing recognition that environmental, ecological, and human systems are linked inextricably in coastal regions. The purpose of this article was to integrate environmental, ecological and human dimensions information important for fisheries management into a common analytical framework. We then used the framework to examine the linkages between these traditionally separate subject areas. We focused on synthesis of linkages between the Gulf of Alaska marine ecosystem and human communities of practice, defined as different fisheries sectors. Our specific objective was to document the individual directional linkages among environmental, ecological, and human dimensions variables in conceptual models, then build qualitative network models to perform simulation analyses to test how bottom-up and top-down perturbations might propagate through these linkages. We found that it is both possible and beneficial to integrate environmental, ecological, and human dimensions information important for fisheries into a common framework. First, the conceptual models allowed us to synthesize information across a broad array of data types, representing disciplines such as ecology and economics that are more commonly investigated separately, often with distinct methods. Second, the qualitative network analysis demonstrated how ecological signals can propagate to human communities, and how fishery management measures may influence the system. Third, we found that incorporating multi-species interactions changed outcomes because the merged model reversed some of the ecological and human outcomes compared with single species analyses. Overall, we demonstrated the value of linking information from the natural and social sciences to better understand complex social–ecological systems, and the value of incorporating ecosystem-level processes into a traditionally single species management framework. We advocate for conceptual and qualitative network modelling as efficient foundational steps to inform ecosystem-based fisheries management.