Salinity is an influential abiotic environmental factor in aquatic species, specifically in freshwater, where salinization causes ecosystem degradation. Secondary salinization, that is increases in salinity due to anthropogenic activities, can affect both osmoregulation and behaviour in freshwater fishes. It is generally believed that invasive species handle climatic change and environmental degradation better than native species, which is one reason for their invasion success. However, how invasive and native species cope with salinity changes remains little understood. Therefore, we investigated how low (500 µS/cm) and high salinity (2000 µS/cm) conditions affected oxygen consumption and behaviour in the invasive round goby (Neogobius melanostomus) and the native European perch (Perca fluviatilis). Our results showed that in round goby oxygen consumption increased and swimming and non-swimming movements changed in response to salinity increments, whereas European perch was not affected by salinity. Thus, it seems as if the invasive round goby is more sensitive to changes in salinity than the native European perch. Our results fit with the minority of studies indicating invasive species being less tolerant than some native species to environmental changes. This finding could be explained by the adaptation of round goby to low salinity due to its long establishment in River Rhine. Further, our results are also confirming that the effect of salinity is species-specific. In addition, European perch and round goby show diametrically different behavioural response to disturbance which could be an effect of holding different ecological niches as well as their anatomical differences.