Flow regulation and the spread of invasive species are significant threats to freshwater biodiversity, including native fish communities in rivers across the globe. The bleak (Alburnus alburnus), an invasive fish currently widespread throughout the main rivers of the Iberian Peninsula, threatens native fish biodiversity, mostly via trophic competition and hybridisation. In this study, we assessed the impacts of bleak presence and rapid flow fluctuations (both main and interactive effects) on the use of artificial habitats (a flow refuge) and the stress physiology of barbels. We examined how bleak's presence influenced the selection of flow refuges by the native Iberian barbel (Luciobarbus bocagei) under base (continuous 7 L s−1 flow stimulus) and pulsed (7 L s−1 to a 60 L s−1 pulse) flows in an indoor flume. We quantified habitat use within three specific regions of two installed flow refuges and two physiological responses (glucose and lactate) associated with the stress axis. The results indicated that the presence of bleak significantly reduced flow refuge use by barbels and this effect was more prominent during pulsed flows. Additionally, barbels exhibited higher levels of glucose and lactate in the presence of bleaks. These results show that bleaks compete with barbels for habitat under fluctuating flows and induce physiological adjustments that may reduce the ability of barbels to find low-velocity areas to shelter. Overall, the bleaks had a competitive advantage under high flow variability. This underscores the need for further studies and effective management strategies to protect native freshwater fish communities in the context of biological invasions and anthropogenic flow variability.