Non-native species can cause negative impacts when they become invasive. This study entails a comparison of risk classifications for 25 aquatic non-native species using various European risk identification protocols. For 72% of the species assessed, risk classifications were dissimilar between countries. The pair-wise comparison of Freshwater Fish Invasiveness Scoring Kit (FISK) scores of in total 28 fish species from the UK, Flanders (Belgium) and Belarus resulted in a higher correlation for scores of Flanders-Belarus than that of Flanders-UK and Belarus-UK. We conclude that different risk classifications may occur due to differences in (1) national assessment protocols, (2) species-environment matches in various biogeographical regions, and (3) data availability and expert judgement. European standardisation of risk assessment protocols, performance of biogeographical region specific risk classifications and further research on key factors for invasiveness of aquatic ecosystems are recommended.