Habitat structure at many scales influences faunal communities. Although habitat structure at different scales often covaries, studies rarely examine the relative effects of structure at multiple scales on faunal density and diversity. In shallow-water seagrass systems, epifaunal density at local scales generally increases with increased habitat structural complexity (e.g. shoot density per unit area). In turn, structural complexity often varies with other aspects of habitat structure at patch scales, such as proximity to patch edges, which itself modifies ecological processes that structure epifaunal communities. We conducted surveys and a manipulative experiment in the eelgrass Zostera marina beds of San Diego Bay, California, USA, to determine (1) whether eelgrass structural complexity, epifaunal density and diversity, and fish (predator) density and diversity vary with proximity to patch edges, and (2) the relative influences of structural complexity, proximity to patch edges and predator presence on epifaunal distribution. Seagrass structural complexity generally increased from patch edges to patch interiors at all sites and in all sampling periods. However, patterns of epifaunal density, diversity, and biomass varied among sites and sampling periods, with density and biomass increasing from patch edges to interiors at some sites and decreasing at others. In the manipulative experiment, we allowed epifauna to colonize sparse or dense artificial seagrass habitat at both the edge and interior of a seagrass patch, and enclosed a subset of experimental units in predator exclusion cages. Overall, proximity to patch edges had a larger influence on epifaunal density and community structure than did structural complexity or predation, with the exception of some common taxa which responded more strongly to either complexity or predator exclusion. Our results emphasize the importance of addressing and evaluating habitat structure at multiple scales to better understand the distribution and interactions of organisms in a particular environment.