The Guana Tolomato Matanzas reserve is one of 28 National Estuarine Research Reserves (GTMNERR) encompassing approximately 73,300 acres of salt marsh and mangrove tidal wetlands, oyster bars, estuarine lagoons, upland areas, and offshore ocean waters along the northeastern coast of Florida in St. Johns and Flagler Counties (Figure 1). The reserve consists of a northern and southern component separated geographically by the City of St. Augustine. The northern component includes the Tolomato and Guana River estuaries and adjacent offshore waters and the southern component contains the Matanzas River. The GTM-NERR, managed under a partnership between the National Oceanic and Atmospheric Administration (NOAA) and Florida Department of Environmental Protection (DEP), was established to promote ‘conservation of natural biodiversity and cultural resources through research and monitoring to guide science-based stewardship and education strategies’. A NERR System-Wide Monitoring Program (SWMP) was developed to improve fundamental understanding of the temporal and spatial dynamics of estuarine processes and to provide baseline information for evaluating change in ecosystem function in response to natural and human disturbances (NERRS 2011). Although water-quality monitoring has been a major focus of SWMP at GTM and other NERR locations, additional research efforts of various partnering institutions provide a variety of other complementary data to help address NERRS science and management needs. Accordingly, a study was initiated in summer 2014, through collaborative efforts by NOAA’s National Centers for Coastal Ocean Science (NCCOS) and GTM-NERR staff, to assess the status of ecosystem condition and potential stressor impacts throughout submerged (subtidal, with the exception of intertidal oyster) habitats of the GTM reserve using multiple indicators of ecological condition. Results, reported herein, are intended to help address priority science and management research gaps identified in the GTM-NERR Site Profile and Management Plan, including characterization of submerged habitats and associated living resources, biological monitoring with measures of biodiversity and condition, and GIS-based mapping of submerged habitats to serve as baselines for future change analysis.