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We study the dynamics of the planktonic ecosystem in the coastal upwelling zone within the California Current System using a three-dimensional (3-D), eddy-resolving circulation model coupled to an ecosystem/biogeochemistry model. The physical model is based on the Regional Oceanic Modeling System (ROMS), configured at a resolution of 15 km for a domain covering the entire US West Coast, with an embedded child grid covering the central California upwelling region at a resolution of 5 km. The model is forced with monthly mean boundary conditions at the open lateral boundaries as well as at the surface. The ecological/biogeochemical model is nitrogen based, includes single classes for phytoplankton and zooplankton, and considers two detrital pools with different sinking speeds. The model also explicitly simulates a variable chlorophyll-to-carbon ratio. Comparisons of model results with either remote sensing observations (AVHRR, SeaWiFS) or in-situ measurements from the CalCOFI program indicate that our model is capable of replicating many of the large-scale, time-averaged features of the coastal upwelling system. An exception is the underestimation of the chlorophyll levels in the northern part of the domain, perhaps because of the lack of short-term variations in the atmospheric forcing. Another shortcoming is that the modeled thermocline is too diffuse, and that the upward slope of the isolines toward the coast is too small. Detailed time-series comparisons with observations from Monterey Bay reveal similar agreements and discrepancies. We attribute the good agreement between the modeled and observed ecological properties in large part to the accuracy of the physical fields. In turn, many of the discrepancies can be traced back to our use of monthly mean forcing. Analysis of the ecosystem structure and dynamics reveal that the magnitude and pattern of phytoplankton biomass in the nearshore region are determined largely by the balance of growth and zooplankton grazing, while in the offshore region, growth is balanced by mortality. The latter appears to be inconsistent with in situ observations and is a result of our consideration of only one zooplankton size class (mesozooplankton), neglecting the importance of microzooplankton grazing in the offshore region. A comparison of the allocation of nitrogen into the different pools of the ecosystem in the 3-D results with those obtained from a box model configuration of the same ecosystem model reveals that only a few components of the ecosystem reach a local steady-state, i.e. where biological sources and sinks balance each other. The balances for the majority of the components are achieved by local biological source and sink terms balancing the net physical divergence, confirming the importance of the 3-D nature of circulation and mixing in a coastal upwelling system.