Through monitoring using molecular and conventional techniques novel data on the distribution and number of non-indigenous species (NIS) are provided for the Danish Wadden Sea area. Review of existing data sources, including the national monitoring program for marine species, enabled a description of changes in NIS occurrences over time, and updated information on the total number of NIS in the region, for which we applied an expert-based judgement to identify high impact NIS. Combining a literature review on introduction pathways for the observed NIS with a model tracer-based assessment of NIS dispersal, helped identify the importance of different introduction pathways. This information was finally used to identify the possible and suitable mitigation responses for NIS in the Danish Wadden Sea.