The objectives of the present work are to relate the spatial distribution of benthic macrofauna in the Baltic Sea to patterns in environmental variables describing near-bottom hydrographical conditions and sediment characteristics, analyzing the data for two various spatial extents. It is mainly based on data from Benthos Databank of the Leibniz Institute for Baltic Sea Research (IOW). Other data considered originated from various available databases and historical data on distribution of macrobenthic species. The first case study is devoted to an exploratory statistical description of the prevailing ecological structure within the limited area attached to the region of the Mecklenburg Bight. Species-specific models predicting the probability of occurrence relative to environmental and sedimentological characteristics were developed for 29 representative macrofaunal species using a logistic regression modelling approach. Finally, the investigation proceeded on a large spatial scale. The discriminating ability of such factors as salinity, bathymetry and sediment characteristics to explain the occurrence of typical macrozoobenthic species on the Baltic Sea-wide extend was tested.