A 3-D physical and biological model is used to study the seasonal dynamics of physical and biological processes in the central California Current System. Comparisons of model results with remote sensing and in situ observations along CalCOFI Line 67 indicate our model can capture the spatial variations of key variables (temperature, nutrients, chlorophyll, and so on) on annual mean and seasonal cycle. In the coastal upwelling system, it is the alongshore wind stress that upwells high nutrients to surface from 60 m and stimulates enhanced plankton biomass and productivity in the upwelling season. As a result, coastal species peak in the late upwelling period (May–July), and oceanic species reach the annual maxima in the oceanic period (August–October). The annual maximum occurs in the late upwelling period for new production and in the oceanic period for regenerated production. From the late upwelling period to the oceanic period, stratification is intensified while coastal upwelling becomes weaker. Correspondingly, the coastal ecosystem retreats from ∼300 to ∼100 km offshore with significant decline in chlorophyll and primary production, and the oceanic ecosystem moves onshore. During this transition, the decline in phytoplankton biomass is due to the grazing pressure by mesozooplankton in the 0–150 km domain, but is regulated by low growth rates in the 150–500 km offshore domain. Meanwhile, the growth rates of phytoplankton increase in the coastal waters due to deeper light penetration, while the decrease in offshore growth rates is caused by lower nitrate concentrations.