In this thesis, I investigate the organization of eelgrass (Zostera marina L.) and mesograzer communities across local and regional scales in three upwelling- influenced estuaries located along the Oregon coast, USA. Eelgrass ecosystems are an important source of primary production in estuarine systems, providing numerous ecosystem services, including nursery habitat for commercial fish, water quality improvement, and sediment stabilization. Community structure in eelgrass systems, i.e., the diversity, abundance, and composition of primary and secondary consumers, is influenced by a combination of local to regional scale variability in environmental and biotic factors. Thus, an important consideration in the management of these systems is to understand the organization of community structure across spatiotemporal scale and the implications for top-down (consumer) versus bottom-up (resource) control. In upwelling-influenced estuaries of the Pacific Northwest coast of the United States, eelgrass systems are exposed to latitudinal variability in oceanographic inputs, but the degree to which these regional effects versus local effects organize eelgrass community structure is poorly understood. Here I investigate the relationship between primary producers (eelgrass, ulvoid macroalgae, and epiphytes), epifauna mesograzers, and fish predators within and across three estuaries located on the Oregon Coast, USA (Netarts Bay, Yaquina Bay, and Coos Bay). Specifically, I asked: 1) What is the relative importance of local (within estuary) versus regional (across estuaries) scale patterns to eelgrass community structure (i.e., primary producers, epifaunal mesograzers, and fishes) in upwelling-influenced estuaries in Oregon?, 2) What is the potential role of regional oceanography versus trophic interactions in regulating eelgrass community structure, and is this dependent on spatial scale?, and 3) What are the management implications for eelgrass communities when regional and local scales are considered?I found that while local effects were important, regional (estuary) scale patterns strongly influenced community structure in eelgrass communities, providing support that regional oceanographic bottom-up forcing dominates eelgrass communities. Additionally, I found evidence for top-down control by the opisthobranch Phyllaplysia taylori on primary producers at one site within Netarts Bay. I suggest that eelgrass beds in these estuaries are mostly bottom-up systems, and further investigations should focus on quantifying the mechanistic relationship between mesograzers and primary producers at local to regional scales.