A large-eddy simulation model developed at the National Center for Atmospheric Research (NCAR) is extended to simulate the transport and diffusion of C¹⁸OO, H₂¹⁸O and ¹³CO₂ in the atmospheric boundary layer (ABL). The simulation results show that the ¹⁸O compositions of leaf water and the ABL CO₂ are moderately sensitive to wind speed. The variations in the ¹⁸O composition of water vapour are an order of magnitude greater than those in the ¹³C and ¹⁸O compositions of CO₂ both at turbulent eddy scales and across the capping inversion. In a fully-developed convective ABL, these isotopic compositions are well mixed as with other conserved atmospheric quantities. The Keeling intercepts determined with the simulated high-frequency turbulence time series do not give a reliable estimate of the ¹⁸O composition of the surface water vapour flux and may be a reasonable approximation to the ¹³C and ¹⁸O compositions of the surface CO₂ flux in the late afternoon only after a deep convective ABL has developed. We suggest that our isotopic large-eddy simulation (ISOLES) model should be a useful tool for testing and formulating research hypotheses on land–air isotopic exchanges.