The predicted global warming of surface waters can be challenging to aquatic ectotherms like freshwater mussels. Especially animals in northern temperate latitudes may face and physiologically acclimate to significant stress from seasonal temperature fluctuations. Na+/K+-ATPase enzyme is one of the key mechanisms that allow mussels to cope with changing water temperatures. This enzyme plays a major role in osmoregulation, energy control, ion balance, metabolite transport and electrical excitability. Here, we experimentally studied the effects of temperature on Na+/K+-ATPase activity of gills in two freshwater mussel species, Anodonta anatina and Unio tumidus. The study animals were acclimated to three ambient temperatures (+4, +14, +24 °C) and Na+/K+-ATPase activity was measured at those temperatures for each acclimation group. Both species had their highest gill Na+/K+-ATPase activity at the highest acclimation temperature. Na+/K+-ATPase activity of gills exhibited species-specific differences, and was higher in A. anatina than U. tumidus in all test groups at all test temperatures. Temperature dependence of Na+/K+-ATPase was confirmed in both species, being highest at temperatures between +4 and + 14 °C when Q10 values in the acclimation groups varied between 5.06 and 6.71. Our results underline the importance of Na+/K+-ATPase of gills for the freshwater mussels in warming waters. Because Na+/K+-ATPase is the driving force behind ciliary motion, our results also suggest that in warming waters A. anatina may be more tolerant at sustaining vigorous ciliary action (associated with elevated respiration rates and filter-feeding) than U. tumidus. Overall, our results indicate great flexibility of the mussel's ecophysiological characteristics as response to changing conditions.