Stable water isotope tracers (HDO and H218O) are incorporated into the ModelE version of the Goddard Institute for Space Studies Atmospheric (GISS) General Circulation Model (GCM). Details of the moist convective parameterisation, cloud phase, background ozone, isotope kinetics and vertical resolution are varied and we examine their impacts, particularly in the upper troposphere (UT) and lower stratosphere. We find that isotopes in precipitation, except in Antarctica, are largely unaffected by these changes and thus are not a useful metric for evaluating model skill above the lower troposphere. Simulated isotopic entry values into the stratosphere over all experiments range between -750 and -600? for HDO, and -130 to -90? for H218O, demonstrating that the mixing processes simulated by the model can explain a significant part of the observed offset from pure Rayleigh distillation. Isotope fields are shown to be sensitive to the parameterisation of cloud physics and representation of UT processes and therefore may be useful in constraining modeled cloud physics and mechanisms of stratosphere-troposphere water vapour exchange.