One of the objectives of monitoring benthic algal cover is to observe short- and long-term changes in species distribution and structure of coastal benthic habitats as indicators of ecological state. Mapping benthic algal cover with conventional methods (diving) provides great accuracy and high resolution, yet is very expensive and is limited by the time and manpower necessary. We measured reflectance spectra of three indicator species for the Baltic Sea: Cladophora glomerata (green macroalgae), Furcellaria lumbricalis (red macroalgae), and Fucus vesiculosus (brown macroalgae) and used a bio-optical model in an attempt to estimate whether these algae are separable from each other and sandy bottom or deep water by means of satellite remote sensing. Our modelling results indicate that to some extent it is possible to map the studied species with multispectral satellite sensors in turbid waters. However, the depths where the macroalgae can be detected are often shallower than the maximum depths where the studied species usually grow. In waters deeper than just a few meters, the differences between the studied bottom types are seen only in band 2 (green) of the multispectral sensors under investigation. It means that multispectral sensors are capable of detecting difference in brightness only in one band which is insufficient for recognition of different bottom types in waters where no or few in situ data are available. Configuration of MERIS spectral bands allows the recognition of red, green and brown macroalgae based on their spectral signatures provided the algal belts are wider than MERIS spatial resolution. Commercial stock of F. lumbricalis in West-Estonian Archipelago covers area where MERIS 300 m spatial resolution is adequate. However, strong attenuation of light in the water column and signal to noise ratio of the sensor do not allow mapping of Furcellaria down to maximum depths where it occurs.