Identifying benthic substrates is important to researchers studying aquatic organisms in fresh and salt water systems. Benthic substrates are often not visible from the surface making it necessary to find another method to gather these data. Previous research has demonstrated that low cost side-scan sonar is a reliable way to identify hard substrates, such as rock and gravel, in a small, freshwater stream. In this study, the reliability of the side-scan sonar to accurately identify softer substrates such as grass and mud was tested in a large, brackish lagoon system. A total area of 11.55 km2 was surveyed with the sonar. Videos and pictures were taken at various points to groundtruth the sonar images and provide a measure of accuracy. Five substrate types were identified: dense seagrass, sparse seagrass, mangrove soil, mangrove soil with rock, and silt. Unidentifiable substrates were classified as unknown. A manually zoned benthic substrate map was created from the sonar recordings. Dense seagrass was most accurately identified. Sparse seagrass was the least accurately identified. A bathymetric map was also created from the sonar recordings.