River ecosystems are exposed to a multitude of stressors, including increasing pesticide run-off driven by precipitation and irrigation. Pyrethroids are the fourth major group of insecticides in use worldwide and have extremely negative effects on aquatic fauna. In this study, we aimed to assess the effects of an acute 2 h sub-lethal exposure to different levels of the pyrethroid esfenvalerate on the swimming behaviour of two Cypriniformes species: the native Iberian barbel (Luciobarbus bocagei) and the non-native invasive bleak (Alburnus alburnus). The experimental set-up consisted of previous exposure to three esfenvalerate concentrations (control, 1.2 (low), and 2.0 (high) μg/L) before being stocked in a three-artificial-flume-channel mesocosm for behavioural trials through direct observation. Monitored behaviours included (i) routine activity, (ii) shoal cohesion, and iii) boldness. Significant differences in fish behaviour were detected for the native species (barbel), as individuals spent significantly more time holding position (i.e., resting) in the control (44.9%) than in the high esfenvalerate concentration (25.2%). Concordantly, control barbels were also found to perform more directional changes than the ones exposed to high esfenvalerate concentrations. Behavioural changes were also found for boldness, measured by the proportion of fish attempts to negotiate the upstream ramp, which were significantly higher in the control (37.4%) and in the high concentration (41.5%) compared to the low one (21.1%). Finally, regarding shoal cohesion of the barbel, it was tighter in the control (81.3%) than in the low- (70.5%) and high- (71.1%) esfenvalerate treatments. For the invasive bleak, there were no significant differences in any of the behavioural traits upon previous exposure to an increasing esfenvalerate concentration. This experimental study demonstrated that even short-term exposure to the pyrethroid esfenvalerate was sufficient to alter the behaviour of a native Cypriniformes fish species while not affecting the non-native species. This may confer greater competitive advantages to non-native fish species in the context of global changes.