Abstract Invasive exotic (alien) species have not been taken into enough consideration concerning the European Water Framework Directive (WFD) and other European directives until recently. The Dutch ministry responsible for water management is looking for ways to establish the impacts that invasive alien species may have on specified water types. This paper concentrates on the vulnerability of such water types to the introduction of exotic species. This new approach focusses on the system where the alien species are introduced into rather than only on the alien species themselves. We propose an equation that combines threats to and in water types with effects of particular species (observed or prognosticated). Numerical values used in the formula have been found by scoring a number of properties in different water types and species, which are specified in questionnaires. The results of the calculations are given as relative vulnerability scores (scale 1–10). By testing as many as 8 water types and 13 species, we demonstrate that this method is flexible and easy to use for water managers. Our results can be translated into classes of vulnerability, which are represented on geographical maps with colour codes to indicate different degrees of vulnerability in the different water bodies. This readily corresponds to the way countries are required to report to the European Union in the context of the WFD. The method can also be generalized using functional groups of (exotic) species instead of particular species.