The low-frequency dynamics of coastal upwelling and cross-shelf transport in the Central and Southern California Current System (CCS) are investigated using the Regional Ocean Modeling System (ROMS) over the period 1965-2008. An ensemble of passive tracers released in the numerical model is used to characterize the effects of linear (Ekman upwelling) and non-linear (mesoscale eddies) circulation dynamics on the statistics of advection of coastal waters. The statistics of passive tracers released in the subsurface show that the low-frequency variability of coastal upwelling and cross-shelf transport of the upwelled water mass are strongly correlated with the alongshore wind stress, and are coherent between the central and southern CCS. However, the offshore transport of tracers released at the surface is not coherent between the two regions, and is modulated by intrinsic mesoscale eddy activity, in particular cyclonic eddies. The transport of cyclonic eddies extends with depth and entrains water masses of southern origin, advected by the poleward California Undercurrent (CUC). The CUC water masses are not only entrained by eddies but also constitute a source for the central California upwelling system. The interplay between intrinsic (eddy activity) and deterministic (Ekman upwelling) dynamics in controlling the cross-shelf exchanges in the CCS may provide an improved framework to understand and interpret nutrients and ecosystem variability