We investigate decadal variations in the three-dimensional structure of the California Current System (CCS) upwelling cells as a potential mechanism for explaining observed ecosystem changes after the mid-1970s. To this end, we track the origin of upwelled water masses using adjoint passive tracers during time periods corresponding to the positive and negative phase of the Pacific Decadal Oscillation (PDO) in a 55 year regional ocean model simulation of the CCS. Results show that in the PDO “cool” phase (pre mid-1970s), the upwelling cell is deeper while during the “warm” phase (post mid-1970s), the upwelling cell is shallower with more horizontal entrainment of surface waters from the north. These changes in the coastal upwelling cell exhibit a latitudinal non-uniformity and may result in significant changes of the nutrient flux, which would have important impacts on the biological productivity of the coastal ocean.