Using nutrient budgets, it has been proven that atmospheric deposition of Mg and Ca sustains the fertility of forest ecosystems on base-poor soils. However the fate of this nutrient input within the ecosystem was presently unknown. Our hypothesis is that the biological cycling of these nutrients is very rapid and conservative to prevent further Mg and Ca losses most especially in ecosystems on base-poor soils. Stable isotopes of magnesium and calcium (Mg-26 and Ca-44) were used to trace the dynamics of throughfall Mg and Ca in the forest soil of a 35-year-old beech stand. The aim of the present study was to (1) understand the processes and the velocity of the incorporation of tracers in the biogeochemical cycles and (2) compute Mg and Ca budgets for the ecosystem by isotope dilution. Rainfall Mg and Ca were strongly and rapidly retained mainly by ion exchange in the thin OL litter-layer. However, Ca was much more strongly retained in the litter-layer than Mg. As a result, 2 years after the application of tracers (2012), 92 % of Mg-26 and 67 % of Ca-44 was released and transferred to the soil or taken up by trees. The vertical transfer of Mg was very slow only 15 % of Mg-26 was found below 15 cm depth in 2012. Ca was slower than Mg-26 only 9 % of Ca-44 was found below 5 cm depth. Although matrix flow was the main vertical transfer process of Ca and Mg, preferential transfer in macropores occurred. Overall, Mg was more rapidly leached through the soil profile than Ca because the soil CEC was mainly composed of organic charges which affinity for Ca is much higher than for Mg. 27 % of Mg-26 and 20 % of Ca-44 was found in tree biomass and total tracer recovery was close to 100 %. These results suggest that no tracers were lost to drainage over the 2 years. Finally, applying the isotopic dilution theory to the whole-ecosystem enabled us to estimate Mg and Ca budgets -0.9 kg ha(-1) year(-1) for Mg, which was close to computed input-output budgets -0.8 and 0 kg ha(-1) year(-1) for Ca, which was very different from input-output budgets (-3.1 kg ha(-1) year(-1)). Our results suggest that a Ca source is underestimated or not taken into account. Over all, organic matter of the litter-layer and in the soil profile played an essential role in the retention of throughfall Mg and Ca and their cycling within the forest ecosystem.