Small pelagic fish represent a critical trophic link between plankton and large predators in marine upwelling ecosystems such as the California Current System. Populations of these fish are highly variable over time and are characterized by extreme fluctuations in abundance, which have significant ecosystem impacts. The causes driving this instability are not well understood, but several climactic and ecological factors have been hypothesized. This research investigated the linkages between habitat, plankton prey resources, and the abundance and behavior of small pelagic fish at various temporal and spatial scales (i.e., daily, weekly patterns of wind-driven upwelling, and seasonal) to understand how changes in physical and prey habitats influence trophic interactions. This research utilized a combination of stationary and shipboard acoustics, net sampling, and physical oceanography sampling approaches. A comparison of diel schooling behavior and zooplankton availability off Oregon and Monterey Bay, California revealed that changes in fish aggregation behaviors were caused by different timings of zooplankton availability in each region attributable to the extent of zooplankton diel vertical migrations. An analysis of the spatial relationships of acoustic scatterers across ocean fronts caused by wind-driven coastal upwelling indicated that upwelling may lead to a spatial mismatch between small plankton prey and schooling fish that select habitat based on their preference of warmer temperatures. The temporal patterns of zooplankton and pelagic fish abundance near the Columbia River plume were identified, finding that the seasonal appearance of small pelagic fish occurred very abruptly. The timing of fish arrival was poorly correlated with zooplankton abundance but was strongly linked with temperature, salinity, and river flow. Zooplankton abundance was highly variable with very large spikes occurring with the passage of tidally-driven river fronts. This research on the ecological and environmental factors between habitat, plankton, and small pelagic fish has revealed that both the physical habitat and prey fields play an important role in determining these interactions. Variability in the trophic interaction between small pelagic fish and zooplankton over varying scales has important ecosystem consequences, including the potential availability of these prey resources to larger predators, as well as impacts for management.