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Ecosystem-based management (EBM) is increasingly seen as the new paradigm for managing the use of marine resources and ecosystems. Although EBM has been defined in theory, its implementation has faced challenges worldwide. This research aims to examine two approaches to contribute to the operationzalization of EBM by incorporating stakeholder values in the decision-making process, and by better representing ecosystem dynamics in ecosystem models. First, I illustrate a decision-making framework for EBM rooted in structured decision-making (SDM), a well-known systematic approach for planning and stakeholder-consultation processes. SDM helps to identify the values of the constituents and define objectives and indicators that are consistent with those values. I demonstrate how SDM can enable managers to evaluate the performance of management alternatives using indicators specifically chosen to reflect values. This can help managers make more systematic, transparent and informed decisions with respect to the use of marine resources. As a case study, I apply SDM to the marine planning process on the west coast of Vancouver Island (WCVI). Second, as ecosystem models play an important role in EBM, I strive to improve the representation of marine ecosystems using ecosystem models in Ecopath with Ecosim (EwE). I focus on incorporating mediating effects and species reintroductions, both common situations that can strongly influence ecosystem dynamics. These considerations are essential when applying holistic approaches to management but they are not generally included in EwE. I use EwE to model the reintroduction of sea otters (Enhydra lutris) and the mediating effects provided by kelp forests in nearshore ecosystems of the WCVI. Because EwE does not have the functionality to represent reintroductions, I created two scenarios to work around the assumptions of Ecospace on the initial state of the ecosystem. In addition, I demonstrate how mediating effects can be represented using the ‘mediation’ function in Ecosim. These methods and results can contribute to advance EBM on the WCVI and offer insights to other marine planning processes. Both strengths and limitations of this work are presented and analyzed.