In fresh waters, non-native invertebrate species preferentially spread via navigation waterways, where they often dominate assemblages. Littoral habitats in navigation waterways are regularly exposed to ship-induced waves. We conducted experiments to test the effects of artificial wave exposure on the relative performance of wide-spread native and non-native species. We compared physiological and behavioural response variables (i.e. growth rate, glycogen content, feeding and swimming activity) of two amphipods (native Gammarus roeselii and non-native Dikerogammarus villosus) and two gastropods (native Bithynia tentaculata and non-native Physella acuta) subject to wave and control (i.e. no wave) treatment flumes across a 6-week period. Growth, and in part glycogen content (as a measure of energy storage), were significantly reduced after exposure to waves in native invertebrates, but not in non-native invertebrates. The reduction in growth may be associated with the disturbance effects of waves, such as the higher swimming activity of G. roeselii and lower food uptake of B. tentaculata. In comparison, the effective hiding behaviour observed for D. villosus and good swimming ability of P. acuta, were identified as important traits facilitating the successful colonisation of the harsh habitat conditions of littoral waterways. Our study demonstrates that artificial wave regimes may contribute significant selective pressure, thus explaining the observed dominance of non-native species in navigational waterways. The success of non-native species under the harsh hydraulic habitat conditions of these socio-economically driven ecosystems may consequently be traced directly to behavioural and/or physiological traits.