Water isotopes are tracers of convective processes and are often used as proxies for past precipitation. These applications require a better understanding of the impact of convective processes on the isotopic composition of water vapor and precipitation. One way to advance this understanding is to analyze the isotopic mesoscale variations during organized convective systems such as tropical cyclones or squall lines. The goal of this study is to understand these isotopic mesoscale variations with particular attention to isotopic signals in near-surface vapor and precipitation that may be present in observations and in paleoclimate proxies. With this aim, we run cloud resolving model simulations in radiative-convective equilibrium in which rotation or wind shear is added, allowing us to simulate tropical cyclones or squall lines. The simulations capture the robust aspects of mesoscale isotopic variations in observed tropical cyclones and squall lines. We interpret these variations using a simple water budget model for the sub-cloud layer of different parts of the domain. We find that rain evaporation and rain-vapor diffusive exchanges are the main drivers of isotopic depletion within tropical cyclones and squall lines. Horizontal advection spreads isotopic anomalies, thus reshaping the mesoscale isotopic pattern. This study contributes to our understanding of mesoscale isotopic variability and provides physical arguments supporting the interpretation of paleoclimate isotopic archives in tropical regions in terms of past cyclonic activity.