Non-indigenous species introduced to marine areas through the release of ballast water may exhibit a threat to European marine ecosystems. Non-indigenous species are explicitly mentioned in the Marine Strategy Framework Directive as a qualitative descriptor of Good Environmental Status and therefore methodologies are needed for understanding, quantifying and mapping the vulnerability of marine waters towards the potential impact of introductions. This risk of a marine area receiving non-indigenous species varies between localities due to numerous factors affecting the probability of survival of individual organisms and subsequently successfully establishing of sustainable populations. One important factor is the connectivity of marine areas, i.e. the likelihood that an organism once released from ballast water in one area ends up in another area. For small organisms (e.g. planktonic species, pelagic larvae of benthic invertebrates or juvenile fish) connectivity is primarily determined by the sea currents and secondarily by species specific life histories and motional behaviour. We have developed a prototype methodology for mapping the connectivity of marine areas of the North Sea region and the western Baltic Sea based on numerical modelling integrating classical 3D hydro-dynamical modelling and agent-based modelling. Dividing the North Sea region into areas of 25x25 kilometres in size, a connectivity index of each area has been calculated to produce a series of ballast water vulnerability maps indicating areas where introduced organisms are more likely than others to spread to other areas. We argue that the methodology applied here may be very suitable for other application of relevance to the MSFD.