The importance of spatial pattern in ecosystems has long been recognized. However, incorporating patchiness into our understanding of forces regulating ecosystems has proved challenging. We used a combination of continuously sampling moored sensors, complemented by shipboard sampling, to measure the temporal variation, abundance and vertical distribution of four trophic levels in Hawaii's near shore pelagic ecosystem. Using an analysis approach from trophic dynamics, we found that the frequency and intensity of spatial aggregations--rather than total biomass--in each step of a food chain involving phytoplankton, copepods, mesopelagic micronekton and spinner dolphins (Stenella longirostris) were the most significant predictors of variation in adjacent trophic levels. Patches of organisms had impacts disproportionate to the biomass of organisms within them. Our results are in accordance with resource limitation--mediated by patch dynamics--regulating structure at each trophic step in this ecosystem, as well as the foraging behaviour of the top predator. Because of their high degree of heterogeneity, ecosystem-level effects of patchiness such as this may be common in many pelagic marine systems.