On interannual and longer time scales, dynamical and biogeochemical fluctuations in the North Pacific are dominated by two modes of variability, namely the Pacific Decadal Oscillation and the North Pacific Gyre Oscillation (NPGO). In this study the regional expression of the NPGO in the California Current System (CCS) is detailed. The statistical relationship between the NPGO index and nearshore wind variability (mostly upwelling favorable) along the U.S. West coast is strongest in the wintertime (December to March) off Central California. Most importantly, NPGO fluctuations are associated with a seasonal shift of 1–2 months in the onset of the upwelling season. Regional numerical simulations show that an early (late) onset of upwelling during the positive (negative) phase of the NPGO leads to a more (less) productive planktonic ecosystem throughout spring and summer, i.e., several months after the direct NPGO effects on the system have ceased. These results bring new light on the California ecosystem variability as observed in atypical years such as 2005 and 2007.