We developed a food web model of central Puget Sound to provide science-based support for ecosystem-based management and to refine our understanding of bottom-up and top-down trophic forcing. Phytoplankton accounted for a large fraction of total biomass, total throughput, and caused considerable bottom-up effects in most functional groups in a dynamic simulation fit to time series data from 1981 to 2000. Top-down control was most apparent in the case of bald eagles (Haliaeetus leucocephalus), which exhibited keystone tendencies and appeared capable of causing trophic cascades. Increasing top-down control in several predator–prey relationships improved model fits to time series data from 1981 to 2000, but not as much as introducing non-equilibrium dynamics (biomass accumulation terms) to several key vertebrates. Fishing had little effect on system dynamics. Our model appears well-suited for addressing strategic, scenario-based questions of how the community as a whole will respond to management actions.