The monitoring of shallow water environments is important for spatial planning of the coastal zone, as reflected in large EU initiatives. However, the efficient monitoring of benthic habitats is difficult and time-consuming. The proposed study investigates new approaches to monitor habitats using acoustic methods. We test the hypotheses that a) different benthic habitats on hard- and soft bottoms have a characteristic surface roughness, b) changing habitat population density and composition affect the surface roughness and c) characteristic roughness and its change over time are detectable by high-frequency acoustic angular backscatter. To test the hypotheses, seafloor roughness at the mm scale and corresponding high-frequency angular backscatter will be measured simultaneously for selected habitats and reference sites over an annual cycle. If the hypotheses are successfully tested, habitat-specific acoustic monitoring methods can be established. Applied from AUV systems, this would allow efficient monitoring of large areas. Efficient monitoring of benthic habitats opens interdisciplinary applications, e.g., within the FONA project to test the correlation between seafloor habitats and the distribution top predators such as birds.