Three-dimensional ecosystem response to wind forcing on the continental shelf off Oregon is studied using a five-component nitrogen-based ecosystem model coupled to a high-resolution circulation model. We investigate, in particular, the influence of time-dependent winds and alongshore variations in shelf topography for summer 2001 during the time period of the Coastal Ocean Advances in Shelf Transport (COAST) field experiment. Over summer 2001 the average southward, upwelling-favorable wind leads to the development of a southward coastal jet and upwelled cold nutrient-rich water over the shelf. A strong influence of the shelf topography is found in the observed and modeled nutrients and plankton, with significant spatial variability associated with interactions of the shelf flow with Heceta Bank. The model results show that the largest mean chlorophyll-a concentrations are located onshore of the coastal jet, while the largest mean zooplankton concentrations are found farther offshore, typically on the offshore side of the jet, except on Heceta Bank. During intermittent downwelling periods the largest concentrations of mean zooplankton and phytoplankton, however, are both inshore of the jet. The 20 day oscillations in the modeled nutrients and plankton, the time lags between the wind stress and these ecosystem components, and the decorrelation timescales of phytoplankton agree with those obtained from mooring and satellite measurements. A detailed analysis of the balance between biological and physical forcing helps to clarify the temporal and spatial response of the ecosystem.