In the Northern California Current (NCC), zooplankton communities show interannual and multiyear shifts in species dominance that are tracked by survival of salmon populations. These zooplankton community changes correlate with the Pacific Decadal Oscillation (PDO) index: a ‘warm-water’ copepod species group is more abundant during warm (positive) phases of the PDO and less abundant during cold (negative) phases; the reverse occurs for a ‘cold-water’ species group. The observed relationship led to the hypothesis that the relative dominance of warm/cold-water copepods in the NCC is driven by changes in the horizontal advection of surface water over different phases of the PDO. To test this hypothesis, variation in surface water advection to coastal regions of the NCC over the period of 1950–2008 was investigated using a Regional Ocean Modeling System (ROMS) and passive tracer experiments, then was compared with zooplankton collected off Oregon since 1996. Results showed that surface water advection varied with the phase of the PDO; the low-frequency component of advection anomalies strongly correlated with copepod species composition (R>0.9). During positive phases of the PDO, current anomalies were northward and onshore, resulting in transport of warmer waters and the associated copepods into the region. During negatives phases, increased equatorward current anomalies led to a copepod community that was dominated by cold-water taxa. Our results support the hypothesis that climate-driven changes in basin-scale circulation controls copepod community composition in the NCC, and demonstrate that large-scale climate forcings downscale to influence local and regional ecosystem structure.