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To assess the long-term (27 yr) effects of sediment aging on stable carbon and nitrogen isotope values (δ¹³C and δ¹⁵N), we used a collection of eight freeze cores of annually laminated (varved) lake sediment collected from 1979 to 2007 in Nylandssjon (northern Sweden). Previous research has shown that 20–23% of carbon and 35% of nitrogen is lost in 27 yr. Material from specific years was compared in the cores, e.g., δ¹³C and δ¹⁵N of the surface varve of the 1979 core was followed in cores retrieved in 1980, 1989, 1993, 2002, 2004, and 2006. δ¹³C increased by 0.4–1.5% during the first 5 yr. After this initial increase, only minor fluctuations were recorded. There is a good correlation between the magnitude in δ¹³C changes and the initial carbon and nitrogen concentrations, indicating that the initial sediment composition is important for the ¹³C fractionation. δ¹⁵N gradually decreased by 0.3–0.7% over the entire 27-yr period. The lack of correlation with the initial sediment composition and the gradual decrease in δ¹⁵N indicates a microbial control on δ¹⁵N change. The diagenetic changes in the stable isotope values that occur in Nylandssjon are small, but of the same magnitude as the down-core variation in the varves deposited 1950–2006. Diagenetic effects should be considered when δ¹³C and δ¹⁵N are used to study organic matter sources or paleoproductivity, especially when dealing with recent trends or small changes. Based on our findings, diagenetic effects for δ¹³C are observed during the first 5–10 yr, whereas no delimitation can be recommended for δ¹⁵N.