Large scale climate indices such as the North Pacific Gyre Oscillation (NPGO) have been linked to variability in both phytoplankton and zooplankton, yet the mechanisms by which they are linked remain unknown. We used a three-dimensional coupled biophysical model, SalishSeaCast, to determine the mechanistic links between the NPGO and plankton dynamics in the Strait of Georgia, Canada. First, we compared bottom-up processes during NPGO positive (cold-phase) and negative (warm-phase) years. Then, we conducted a series of model experiments to determine the effects of the NPGO on local physical drivers by switching individual parameters between a typical warm and cold year. The model showed that higher SST and weaker winds contributed to an earlier increase in spring diatom biomass during warm-phase years. Due to the conditions set up during the spring, warm-phase years exhibited lower overall summer diatom biomass and an earlier shift to nanoflagellate-dominance compared to cold-phase years. Our systematic model experiments revealed that variability in wind-driven resupply of nutrients to the surface waters during the summer had the most significant impact on diatom biomass, and ultimately on the food available to zooplankton grazers. The Z1 and Z2 model classes grazed on a higher proportion of nanoflagellates during the summer of warm-phase years, suggestive of a poorer quality diet consumed during warm years. Results from this study are relevant in the context of other climate signals (e.g., El Niño) favouring weaker winds or increased stratification, which would limit the amount of nutrients being replenished to the surface waters.