Isotope turnover in muscle of ectotherms depends primarily on growth rather than on metabolic replacement. Ectotherms, such as fish, have a discontinuous pattern of growth over the year, so the isotopic signature of muscle (delta13C and delta15N) may only reflect food consumed during periods of growth. In contrast, the liver is a regulatory tissue, with a continuous protein turnover. Therefore, the isotopic composition of liver should respond year round to changes in the isotopic signature of food sources. Therefore, we predicted that (1) Whitefish in Lake Geneva would have larger seasonal variation in the isotopic variation of the liver compared to that of the muscle tissue, and (2) the isotope composition of fish muscle would reflect a long-term image of the isotope composition of the food consumed only throughout the growth period. To test these expectations, we compared the isotope compositions of Whitefish muscle, liver and food in a 20-month study. We found that the seasonal amplitude of isotope variation was two to three times higher in liver compared to muscle tissue. During the autumn and winter, when growth was limited, only the isotopic signature of liver responded to changes in the isotope composition of the food sources. The delta13C and delta15N of muscle tissue only reflected the food consumed during the spring and summer growth period.