The analysis of delta(13)C and delta(18)O in tree-ring archives offers retrospective insights into environmental conditions and ecophysiological processes. While photosynthetic carbon isotope discrimination and evaporative oxygen isotope enrichment are well understood, we lack information on how the isotope signal is altered by downstream metabolic processes. In Pinus sylvestris, we traced the isotopic signals from their origin in the leaf water (delta(18)O) or the newly assimilated carbon (delta(13)C), via phloem sugars to the tree-ring, over a time-scale that ranges from hours to a growing season. Seasonally, variable (13)C enrichment of sugars related to phloem loading and transport did lead to uncoupling between delta(13)C in the tree-ring, and the c(i)/c(a) ratio at the leaf level. In contrast, the oxygen isotope signal was transferred from the leaf water to the tree-ring with an expected enrichment of 27 per thousand, with time-lags of approximately 2 weeks and with a 40% exchange between organic oxygen and xylem water oxygen during cellulose synthesis. This integrated overview of the fate of carbon and oxygen isotope signals within the model tree species P. sylvestris provides a novel physiological basis for the interpretation of delta(13)C and delta(18)O in tree-ring ecology.