Biological invasions attract increasing attention from scientists, policy makers and various management authorities. Consequently, the knowledge-base on non-indigenous species (NIS) continuously expands and so the number and availability of web resources on NIS rises. Currently there are more than 250 websites on NIS, ranging from global to regional and national. Many of these databases began as inventories of NIS, but evolved to include information on NIS origin, introduction history, pathways, vectors, and more. The databases have been used increasingly for scientific analyzes, though key information needs for bioinvasion management and research are only partially met. In this account we describe an advanced information system dealing with aquatic NIS introduced to marine, brackish and coastal freshwater environments of Europe and adjacent regions (AquaNIS). AquaNIS differs substantially from existing NIS information sources in its organizational principles, structure, functionality, and output potential for end-users, e.g., managing aquaculture or ship’s ballast water. The system is designed to assemble, store and disseminate comprehensive data on NIS, and assist the evaluation of the progress made towards achieving management goals. With the coming into force of the EU Marine Strategy Framework Directive and similar legislation addressing the problem of biological invasions, the availability of advanced, scientifically validated and up-to-date information support on NIS is essential for aquatic ecosystem assessment and management. Key issues related to electronic information systems, such as data management principles and long-term database maintenance, are discussed.