In the California Current System, strong mesoscale variability associated with eddies and meanders of the coastal jet play an important role in the biological productivity of the area. To assess the dominant timescales of variability, a wavelet analysis is applied to almost nine years (October 1997 to July 2006) of 1-km-resolution, 5-day-averaged, Sea-viewing Wide Field-of-view Sensor (SeaWiFS) chlorophyll a (chl a) concentration data. The dominant periods of chlorophyll variance, and how these change in time, are quantified as a function of distance offshore. The maximum variance in chlorophyll occurs with a period of ∼100–200 days. A seasonal cycle in the timing of peak variance is revealed, with maxima in spring/summer close to shore (20 km) and in autumn/winter 200 km offshore. Interannual variability in the magnitude of chlorophyll variance shows maxima in 1999, 2001, 2002, and 2005. There is a very strong out-of-phase correspondence between the time series of chlorophyll variance and the Pacific Decadal Oscillation (PDO) index. We hypothesize that positive PDO conditions, which reflect weak winds and poor upwelling conditions, result in reduced mesoscale variability in the coastal region, and a subsequent decrease in chlorophyll variance. Although the chlorophyll variance responds to basin-scale forcing, chlorophyll biomass does not necessarily correspond to the phase of the PDO, suggesting that it is influenced more by local-scale processes. The mesoscale variability in the system may be as important as the chl a biomass in determining the potential productivity of higher trophic levels.