A new method for classifying soft-bottom zoobenthic assemblages along the Finnish coasts (northern Baltic Sea) is presented and tested against traditional physicochemical monitoring data in the complex Archipelago Sea. Although multivariate methods for assessing the state of the marine environment have become widely used, few numerical indices can operate over a wide salinity range. We compare indices currently in use and propose a new index, BBI (brackish water benthic index), for the low-saline and species-poor Baltic coastal waters. BBI offers a salinity-corrected tool for classification of the soft-bottom zoobenthos under the demands of the European Union Water Framework Directive.