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An inventory was made of the alien macroinvertebrates occurring in Flanders. To this end large collections of biological samples were investigated and supplemented with own sampling campaigns. Mainly fresh and brackish surface waters were investigated. Three new macroinvertebrate species for Flanders were discovered. In total 41 alien macroinvertebrates were encountered in fresh and slightly brackish surface waters in Flanders. Additionally, 24 alien macroinvertebrate species have been reported for the Belgian part of the North Sea and its adjacent estuaries. Most alien macroinvertebrates belonged to the crustaceans and molluscs. Over 2,500 samples containing macrocrustaceans were identified to species level, which allowed us to accurately map their distribution in Flanders. Alien species found in the fresh and brackish water environment, mainly originated from the Ponto-Caspian area and North-America followed by Asia and South- and East-Europe. This overview shows that alien macroinvertebrates are widespread and abundantly present in many watercourses in Flanders. Based on observations in neighbouring countries, several additional species are expected to arrive in the near future. A follow-up of the invasive alien species together with a monitoring scheme to detect new incoming species is valuable to estimate the size of the problem and to be able to closely follow their ecological and economic impact This dataset was originally created for research on the spread and impact of alien invasive macroinvertebrate species in Flanders. However, the dataset can be reused for a variety of purposes. However, this being an occurrence dataset, it can be used for understanding species richness, distribution pattern and modelling studies such as ecological niche modelling. In order to enhance the confidence of use, we have documented the metadata as well as subjected the data records to a series of quality assessment and enhancement processes as described in the earlier section quality control description. To allow anyone to use this dataset, we have released the data to the public domain under a Creative Commons Zero waiver (http://creativecommons.org/publicdomain/zero/1.0/). We would appreciate however, if you read and follow these norms for data use (http://www.inbo.be/en/norms-for-data-use) and provide a link to the original dataset (https://doi.org/10.15468/xjtfoo) whenever possible. If you use these data for a scientific paper, please cite the dataset following the applicable citation norms and/or consider us for co-authorship. We are always interested to know how you have used or visualized the data, or to provide more information, so please contact us via the contact information provided in the metadata, email@example.com or https://twitter.com/LifeWatchINBO.