The introduction of alien species (AS) in marine environments is a factor of disturbance that can be viewed as a pollution agent. Using basic information on abundance and distribution of alien species, we developed an index that classifies AS impacts on native species, communities, habitats and ecosystem functioning. This method can be used to evaluate impact at five different levels of biopollution, fitting within the existing schemes for water quality assessment. Both spatial and temporal comparisons are possible. The assessments may also be used to evaluate management performance where avoidance measures were necessary and assist in preventing further unwanted introductions. Such assessments made for the same areas over time provide opportunities for measuring change in biopollution. We have tested the method using four different well-studied areas within the Baltic Sea (brackish to freshwater environments) for two different times, 20 years apart. Further developments of the scheme may be needed to cover some specific cases and taxonomic groups according to their life history.