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Community structure and function in ecosystems are dependent on top-down and bottom-up factors, which vary across local, regional, and temporal scales. In estuaries of the U.S. Pacific Northwest coast, eelgrass (Zostera marina) ecosystems are exposed to latitudinally varying oceanographic inputs in the form of ocean upwelling. Previous research suggests that ocean upwelling is critical to eelgrass and ulvoid macroalgae abundance, but the degree to which secondary producers are controlled by processes at regional vs. local scales is unknown. Here, we consider the relationships among primary producers (eelgrass, ulvoid macroalgae, and epiphytic microalgae), epifaunal mesograzers, and mesopredator fish within and across three Oregon, U.S.A., estuaries during a spring-summer season to examine the role of multiple scales in structuring these communities. Our objectives were to determine the relative importance of local and regional scales in organizing eelgrass communities and the potential of regional oceanography and trophic interactions in regulating patterns of primary producers in this system. We found that regional and seasonal patterns strongly influenced eelgrass community structure, providing support for the hypothesis that regional bottom-up forcing predominantly controls these assemblages. Additionally, local effects were important to the patterns of primary producers, mesograzers, and mesopredator fish at specific sites, suggesting limited top-down control. Regarding management and conservation, the implications of our results are that in these highly productive systems, the potential for consumers to moderate the effects of eutrophication may be limited.