The Northern California Current System experiences highly variable seasonal upwelling in addition to larger basin‐scale variability, both of which can significantly affect its water chemistry. Salinity and temperature fields from a 7 year ROMS hindcast model of this region (43°N–50°N), along with extensive particle tracking, were used to study interannual variability in water properties over both the upper slope and the midshelf bottom. Variation in slope water properties was an order of magnitude smaller than on the shelf. Furthermore, the primary relationship between temperature and salinity anomalies in midshelf bottom water consisted of variation in density (cold/salty versus warm/fresh), nearly orthogonal to the anomalies along density levels (cold/fresh versus warm/salty) observed on the upper slope. These midshelf anomalies were well‐explained ( R 2 = 0.6) by the combination of interannual variability in local and remote alongshore wind stress, and depth of the California Undercurrent (CUC) core. Lagrangian analysis of upper slope and midshelf bottom water shows that both are affected simultaneously by large‐scale alongcoast advection of water through the northern and southern boundaries. The amplitude of anomalies in bottom oxygen and dissolved inorganic carbon (DIC) on the shelf associated with upwelling variability are larger than those associated with typical variation in alongcoast advection, and are comparable to observed anomalies in this region. However, a large northern intrusion event in 2004 illustrates that particular, large‐scale alongcoast advection anomalies can be just as effective as upwelling variability in changing shelf water properties on the interannual scale.

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The California Current System (CCS) is a highly productive region because of winddriven upwelling, which supplies nutrients to the euphotic zone. Numerous studies of the relationship between phytoplankton productivity and wind patterns suggest that an intermediate wind speed yields the most productivity on the shelf. However, few studies have considered the productivity-wind relationship across the entire CCS, including the Northern CCS (north of 42 • N), an unusually productive region with highly variable upwelling-and downwelling-favorable winds. Using satellite chlorophyll concentration from GlobColour together with QuikSCAT and ASCAT winds, we examine the relationship between shelf (shallower than the 150 m isobath) chlorophyll concentration and wind patterns in the Central and Northern CCS. Results from this empirical analysis suggest that while there is a dome-shaped relationship between mean chlorophyll concentration and wind stress for the whole system, the Central CCS and Northern CCS have significantly different relationships, which is evident in the separation between their mean chlorophyll concentration-wind stress curves. The Northern CCS also supports high chlorophyll concentration during downwelling-favorable winds. To understand this difference in chlorophyll concentration-wind stress relationships, results from particle tracking experiments using a ROMS model of the Northern CCS are used to map shelf retention times with respect to wind patterns. These results suggest that on the 1 •-latitude scale, the effect of wind intermittency on retention is minimal in the Northern CCS; however, this result does not disqualify the influence of more complex controls on retention like wind intermittency on smaller spatial scales. Lastly, we present a revised hypothesis to describe the relationship between chlorophyll concentration and wind stress in the CCS that includes the influence of non-upwelling-derived nutrients in the Northern CCS.