Benthic maps provide the spatial framework for many science and management activities in coastal areas such as identification and protection of fish distributions and associated habitat as well as for monitoring changes in benthos and fish communities. To meet this need at Gray's Reef National Marine Sanctuary off the Georgia, U.S.A., coast, we created fine-scale benthic maps by visual interpretation of sonar imagery within a geographic information system. The major bottom types in the sanctuary—flat sand, rippled sand, hard bottom that is sparsely colonized with sessile invertebrates, and densely colonized hard bottom—were delineated through combined analysis of backscatter from side-scan sonar, bathymetry from multibeam sonar, scuba surveys, and video transects. Maps showed that unconsolidated sediments cover 75% of the bottom of this region; 8% occurs as flat sand plains with obvious burrowing and reworking of surface material by mobile benthic invertebrates, whereas 67% occurs as rippled sand without such fauna. The rest of the sanctuary consists of limestone bottom in two types of formations; either flat, sparsely colonized regions (25% of the sanctuary's total area) or as vertical ledges that are densely colonized with a diverse fauna of sessile invertebrates (<1%). Despite their limited area, these 0.5–2-m-tall ledge features harbor the majority of the sanctuary's biodiversity and biomass of both sessile invertebrates as well as ichthyofauna. A modified accuracy assessment procedure was used to account for spatial autocorrelation in the validation data and to separate thematic from positional accuracy. Overall thematic accuracy of maps is 95% for those areas of the map in which thematic accuracy and positional accuracy could be separated (87% of the mapped area). This fine-scale characterization provides a benthic inventory for a marine sanctuary and novel methods for mapping using sonar and accuracy assessment using transects.