Eastern boundary upwelling systems (EBUSs) are among the most ecologically diverse and productive regions in the ocean. EBUSs account for approximately 1\% of the global ocean by area, but yields nearly 20\% of the global fish catch. Thus, consequences to changes in productivity in EBUSs anticipated under climate change span from regional socioeconomic stability to global food security. Ecological responses to wind-driven upwelling in EBUSs have long been studied, yet questions still remain on the controls of the cross-shore (zonal) ecosystem composition. Previous studies indicate that large plankton contribute to a majority of the biomass near the coast, where upwelling supports high levels of productivity, whereas small plankton account for most of the biomass in offshore regions with low productivity. However, little is known about the variations in zonal ecosystem composition with respect to perturbations in the large-scale physical forcing. In this thesis, I present a new quasi-2D, idealized physical model of EBUSs and a size structured ecosystem model, in which an organism’s size is chosen to represent ecological diversity. With this coupled physical-biogeochemical model, we characterize the zonal ecosystem composition and its responses to perturbations. These results are an important step toward understanding the sensitivities of plankton communities and higher food-web structure in EBUSs.