Isotopic discrimination measurements in tree rings are becoming increasingly important estimators of past environmental change. Potential biases inherent to these parameters, including age trend and level offset are, however, not well understood. We here perform measurements on a new millennium-long data set of decadally resolved δ18O and δ13C discrimination from 25 high-elevation pine trees in the Spanish Pyrenees to investigate whether such low-frequency biases exist and how they alter the long-term behavior of derived time series. Alignment of the tree ring data by biological age reveals age trends over the first one to four centuries after germination. On average, isotope values change by −0.089‰ δ18O and +0.064‰ δ13C per decade over the first 100 years of tree growth. This trend persists into the forth century after germination for δ18O but diminishes to ∼0‰ over the 100–390 year period for δ13C. We also find level offsets up to 7‰ δ18O and 3‰ δ13C between single trees. Analysis of the shape of age trends reveals negative exponential functions as reasonable choices for detrending of δ18O and (inverted) δ13C time series. The detrended isotope chronologies share low-frequency variance with traditional ring width and density measurements beyond statistical chance, suggesting that the various parameters reflect some of the same environmental forcing. Our results show that δ18O and δ13C from these Spanish pines need to be detrended to assess long-term environmental changes. To evaluate the general applicability of this conclusion, production of (1) well-replicated, (2) nonpooled, and (3) composite chronologies from other species and regions will be required. Increases in measurement speed and technology will make these tests feasible in the coming years.