Sargassum forests play an important role in coastal waters as habitats for marine organisms, including commercial species. However, human activities have negatively affected their distribution causing a worldwide decline of Sargassum forests. Mapping and monitoring the distribution and biomass of these habitats using acoustic remote sensing techniques is key for their conservation. Nonetheless, most researches based on acoustic remote sensing methods focus on estimations of macrophyte area and its canopy height, and less researches reporting 3D visualization of these habitats. This study demonstrates the use of high-resolution multibeam echosounder (MBES) bathymetric data to visualize the 3D structure of Sargassum forests. Comparing acoustic data and underwater camera photos collected in field surveys, we identified Sargassum individuals as vertical clusters of contiguous sounding points with a base close to the sea bottom in the sounding data of the MBES. Using this criterion, we could distinguish Sargassum echoes, visualize the 3D structure of Sargassum forests and estimate the number of Sargassum individuals in the survey area. Using the relation between thallus length and dry weight of sampled Sargassum plants, standing stock and biomass could be estimated assuming the thallus length was the height of Sargassum plants identified with the MBES.