Changes in environmental salinity challenge fish homeostasis and may affect physiological performance, such as swimming capacity and metabolism, which are important for foraging, migration, and escaping predators in the wild. The effects of salinity stress on physiological performance are largely species specific, but may also depend on intra-specific differences in physiological capabilities of sub-populations. We measured critical swimming speed (Ucrit) and metabolic rates during swimming and at rest at salinities of 0 and 10 in European perch (Perca fluviatilis) from a low salinity tolerance population (LSTP) and a high salinity tolerance population (HSTP). Ucrit of LSTP was significantly reduced at a salinity of 10 yet was unaffected by salinity change in HSTP. We did not detect a significant cost of osmoregulation, which should theoretically be apparent from the metabolic rates during swimming and at rest at a salinity of 0 compared to at a salinity of 10 (iso-osmotic). Maximum metabolic rates were also not affected by salinity, indicating a modest tradeoff between respiration and osmoregulation (osmo-respiratory compromise). Intra-specific differences in effects of salinity on physiological performance are important for fish species to maintain ecological compatibility in estuarine environments, yet render these sub-populations vulnerable to fisheries. The findings of the present study are therefore valuable knowledge in conservation and management of estuarine fish populations.