This multi-chapter report describes scientific and logistic understanding gained from a 2 year proof-of-concept study in Liberty Bay, a small urban embayment in central Puget Sound, Washington. The introductory chapter describes the regional and local setting, the high-level study goals, the site-specific urban stressors, and the interdisciplinary study approach. Subsequent data chapters describe detailed studies of various components of the Liberty Bay ecosystem: the aquatic environment (Chapter 2), surface and groundwater quantity and quality (Chapter 3), sediment quality (Chapter 4), eelgrass habitat (Chapter 5), carbon and nitrogen sources (Chapter 6), and a statistical model relating herring spawn probability to shoreline attributes (Chapter 7). The final chapter synthesizes knowledge about individual components into a system-wide understanding of how urbanization may affect the Liberty Bay ecosystem. The Liberty Bay study was conducted as part of the U.S. Geological Survey's Coastal Habitats in Puget Sound project, an interdisciplinary collaboration to understand physical and biological processes that affect nearshore ecosystems.