Abstract Responses of ecosystems to elevated levels of atmospheric carbon dioxide (CO2) remain a critical uncertainty in global change research. Two key unknown factors are the fate of carbon newly incorporated by photosynthesis into various pools within the ecosystem and the extent to which elevated CO2 is transferred to and sequestered in pools with long turnover times. The CO2 used for enrichment in many experiments incorporates a dual isotopic tracer, in the sense that ratios of both the stable carbon-13 (13C) and the radioactive carbon-14 (14C) isotopes with respect to carbon-12 are different from the corresponding ratios in atmospheric CO2. Here we review techniques for using 13C and 14C abundances to follow the fate of newly fixed carbon and to further our understanding of the turnover times of ecosystem carbon pools. We also discuss the application of nitrogen, oxygen, and hydrogen isotope analyses for tracing changes in the linkages between carbon, nitrogen, and water cycles under conditions of elevated CO2.