A three-dimensional (3-D) primitive equation model, developed to simulate the circulation features (filaments) observed in the California coastal transition zone (CTZ), was coupled to a nine-component food web model and a bio-optical model. The simulated flow fields from a 3-D primitive equation model are used to advect the constituents of the food web model, which include silicate, nitrate, ammonium, two phytoplankton size fractions, copepods, doliolids, euphausiids, and a detritus pool. The bio-optical model simulates the wavelength-dependent attenuation of the subsurface irradiance field. The overall objective of this modeling study was to understand and quantify the processes that contribute to the spatial and temporal development of nutrient and plankton distributions in the CTZ. The resulting simulated 3-D nutrient, plankton and submarine light fields agree well with those observed within the CTZ. Specifically, high nutrient and plankton biomass occur onshore and within the core of the simulated filament. Variations in the depth of the 1% light level, which result from the simulated plankton distributions, shallows to less than 30 m in regions of high phytoplankton biomass, and deepens to greater than 75 m in regions of low phytoplankton biomass. The onshore and offshore surface carbon flux patterns are similar in shape due to the meander-like flow patterns of the filament; however, the net across-shore area-integrated carbon flux is predominantly offshore. The total 20-day integrated carbon transport for the model domain varies with distance from shore and is highest (35¿109 g C) in the region where the filament circulation pattern develops into an anticyclonic and cyclonic pair of eddies. The annual integrated carbon transport by filaments along the California coast is estimated to be 1.89¿1012 g C. ¿ American Geophysical Union 1996