The Inventory of alien macroinvertebrates in Flanders, Belgium is a species checklist dataset published by Ghent University. It contains information on 73 alien macroinvertebrate species (mostly crustaceans and molluscs) occurring in Flemish aquatic habitats, from inland lakes to coastal harbours at the North Sea. The inventory is the result of the study Boets et al. (2016) (https://doi.org/10.3391/ai.2016.11.2.03 with occurrence data at https://doi.org/10.15468/xjtfoo) where it was originally published as supplementary material. Here it is published as a standardized Darwin Core Archive and includes for each species: the scientific name, higher classification, and stable taxon identifier (in the taxon core), the year of first introduction and last assessment in Flanders (given as a year range in the event date in the distribution extension), coarse habitat information (in the species profile extension) and the pathway(s) of introduction, native range(s), and invasion stage in Flanders (in the description extension). The dataset can be used for researching and managing aquatic invasions or compiling regional and national registries of alien species. Issues with the dataset can be reported at: https://github.com/trias-project/alien-macroinvertebrates We have released this dataset to the public domain under a Creative Commons Zero waiver. We would appreciate it if you follow the GBIF citation guidelines (https://www.gbif.org/citation-guidelines) when using the data. If you have any questions regarding this dataset, don’t hesitate to contact us via the contact information provided in the metadata or via https://twitter.com/trias_project. This dataset was published as open data for the TrIAS project (Tracking Invasive Alien Species http://trias-project.be, Vanderhoeven et al. 2017), with technical support provided by the Research Institute for Nature and Forest (INBO). It is selected as one of the authoritative sources for the compilation of a unified and reproducible checklist of alien species in Belgium.