Habitat structure is thought to be among the most important factors influencing animal communities. Aspects of habitat structure at different spatial scales impact communities in unique ways, so overall community structure is a product of these complex and interwoven processes. In this study we dissected these mechanisms within eelgrass (Zostera marina) epifaunal communities by sampling a variety of both environmental variables and community responses. This allowed us to test which aspects of habitat structure exerted the greatest influence on the density, diversity, and composition of epifauna within an eelgrass landscape. We also used organisms’ functional traits to determine if changes to species composition translated into differences in community-level trait structure, which potentially affects the overall community function. We found that the amount of habitat at small scales, as measured by eelgrass biomass, had the strongest correlation with total epifaunal density and diversity. Community taxonomic composition was driven by the amount of habitat available at larger scales as measured by the percent eelgrass cover in the surrounding landscape. These results demonstrate that the amount of habitat is more important than its configuration, but that the scale at which the amount of habitat is relevant depends on the community characteristic in question. Lastly, our functional trait analysis revealed that community functional composition was robust to changes in habitat structure. This is an encouraging result from a conservation perspective because it suggests that efforts to preserve and restore eelgrass beds that focus on area regardless of configuration can have positive impacts on the epifaunal community.