Ozone formation, transport and detailed horizontal and vertical distributions in the San Joaquin Valley are investigated using a three-dimensional photochemical model in combination with aircraft observations for a four-day period in July of 2000 during the Central California Ozone Study. Four-dimensional data assimilation are used to assimilate hourly wind profiles from a network of 15 radar wind profilers in the area to produce the best flow fields for ozone transport and mixing in the valley. The model successfully produced the complex circulation patterns caused by thermal and terrain forcing. Except for a general cold bias of 1-2 degrees, the simulated temperature structure and evolution in the boundary layer were also in good agreement with the RASS observations at various locations. Strong vertical wind shears associated with a nocturnal low-level jet (with peak speed > 13 m/s between 200-400 m) promoted turbulent mixing in the lowest 500 m at night, leading to NO titration in a relatively deep layer over the valley floor. Observed and modeled ozone profiles showed only small differences at different locations in the valley, indicating relatively strong horizontal mixing and advection by cross-valley winds. Process analyses and sensitivity tests suggested that the distribution of ozone concentrations in the valley depended largely on regional formation and transport and that the emission from the two large urban centers in the valley played relatively small role.