Seagrass ecosystems are some of the most productive coastal habitats in the world. Eelgrass (Zostera marina) is an ecosystem engineer that provides important ecosystem functions and services. In 2010, the National Oceanic and Atmospheric Administration (NOAA) began construction of their Marine Operations Center-Pacific (MOC-P) in Yaquina Bay, Oregon; coupled with this were unavoidable habitat damages, and mitigation included the creation of a transplanted eelgrass bed. The purpose of this project was to assess the recovery of ecosystem structure and function within this transplanted bed using an ecosystem-based approach. Ecological indicators (e.g., eelgrass percent cover, faunal richness and abundance) and environmental variables (e.g., sediment and water quality parameters) were monitored over 12 months at the transplanted mitigation site and two reference sites. Each bed was observed to be unique in structure, predominately driven by physical setting. Eelgrass cover at the mitigation site remained unchanged and significantly lower than at reference sites; however, most faunal indicators within the transplanted eelgrass bed were comparable to those of existing eelgrass beds. During the first year post-transplant, the eelgrass bed within the NOAA MOC-P mitigation site remained stable and was observed to be adequately performing the functions associated with eelgrass ecosystems in the Pacific Northwest. Characterizing the transplanted bed with an ecosystem-based approach allowed us to accurately assess the site's progress toward mitigation goals and provide information important to management of the NOAA MOC-P mitigation site and future eelgrass mitigation efforts.