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Abstract Invasive alien species (IAS) are species whose introduction or spread outside their native range threatens biological diversity, ecosystem functioning, economy, and/or public health. The recent European Union (EU) regulation on the management of IAS emphasizes the need for a consistent approach to alien species assessment that will underpin international measures for the early identification of newly introduced IAS followed by rapid action aimed at the prevention of introduction, spread, and negative impacts. The goals of the present study were (1) to present the risk classifications of 18 aquatic alien species for The Netherlands using the Invasive Species Environmental Impact Assessment protocol, (2) to compare these with available risk classifications made for countries spanning similar climatic and biogeographical regions to the EU, and (3) to provide explanations for inconsistencies between different risk classifications. Five species were classified as high risk: Carassius gibelio (Prussian carp), Cyprinus carpio (common carp), Sander lucioperca (pike‐perch), Cabomba caroliniana (fanwort), and Dreissena rostriformis bugensis (quagga mussel). Of the 14 species with existing risk classifications for countries spanning similar climatic and biogeographical regions to the EU, all but two of the assessed species (C. gibelio and D. rostriformis bugensis) were classified inconsistently. Reasons for these inconsistencies are the application of different risk assessment schemes, application on a national rather than biogeographical scale, differences in the definition and application of criteria, differences in habitat availability, and uncertainties that are intrinsic to risk assessment methodologies. Approaches that increase transparency by highlighting these methodological aspects, normative choices, and uncertainties are vital to the legitimacy of any risk assessment method and will increase acceptance among decision makers, nature managers, and stakeholders.