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With increasing pressure for a more ecological approach to marine fisheries and environmental management, there is a growing need to understand and predict changes in marine ecosystems. Biogeochemical and physical oceanographic models are well developed, but extending these further up the food web to include zooplankton and fish is a major challenge. The difficulty arises because organisms at higher trophic levels are longer lived, with important variability in abundance and distribution at basin and decadal scales. Those organisms at higher trophic levels also have complex life histories compared to microbes, further complicating their coupling to lower trophic levels and the physical system. We discuss a strategy that builds on recent advances in modeling and observations and suggest a way forward that includes approaches to coupling across trophic levels and the inclusion of uncertainty.