Scientific interests on coastal ecosystems are still challenging these days. Here, a special research focus lies on the monitoring of sublitoral vegetation. For instance, kelps (large brown algae) are supposed to form one of the most productive ecosystems in the world, whereas little is known about their spatial and temporal dynamics. Besides the ecological aspect algae are of great interest for industrial utilization. For example, the farming of green and brown algae is widely common on the rocky coasts of South Africa, Thailand and China. Conventional field survey methods are not only time and labor intensive but also terminated to small coastal areas. Therefore, it is essential to apply remote sensing techniques to improve quantitative and qualitative spatial analysis of coastal areas. The aim of this study is to analyze the potential of hyperspectral remote sensing data to identify sublitoral algae species. We concentrate on an approach to classify submerged algae using a water column correction and subsequent spectral unmixing using the Modular Inversion Program (MIP). In summer 2010 a flight campaign was conducted over Helgoland’s shallow waters using the airborne hyperspectral instrument AISAeagle. After preprocessing, the hyperspectral data were atmospherically and water-column corrected using field spectrometer and RAMSES data which were recorded simultaneously to the AISA overflights. To characterize the water body for the correction, in situ measurements for chlorophyll analysis, suspended sediment and dissolved organic carbon (DOC) were taken. For validation purposes algae mappings were conducted by divers within the 10 meters isobaths. After atmospheric and water-column correction bottom sediment and algae reflectance can be separates by spectral unmixing. The results are used to identify submerged algae communities. The approach described above enables a mapping of the coastal sublitoral. Thus, existing remote sensing approaches which normally are restricted to the intertidal zone can be improved significantly. A monitoring of both sublitoral and intertidal coastal zones is one step towards an integrated coastal zone management.