Arsenic contamination of groundwater is observed throughout South and Southeast Asia, affecting the low and flat floodplains of rivers draining the Himalayas. This geogenic contamination exposes over 100 million people to arsenic through their drinking water, posing a major health hazard. Two such affected areas are the Red River and Mekong deltas in Vietnam, where growing population and climate change combine with natural arsenic occurrence to form highly unpredictable spatial and temporal patterns of groundwater contamination. In the context of the DeltAs project, which aims to quantify the temporal and spatial variation of Arsenic in deltaic environments, we develop detailed 3D geological and hydrogeological models of the Red River and Mekong deltas. Each forms a complex coastal aquifer system that is non-negligibly affected by its neighbouring sea. Saline water intrudes both underground, in freshwater aquifers, and overground as a result of subsidence. Tidal and wave action significantly shapes the sedimentation of the delta mouth. Estuarine sediments, different in their composition from landward alluvial depositions, influence the distribution of groundwater arsenic. The hydrogeological modelling of these deltas thus require careful integration of the land-ocean transition zone. We present here the current state of both the Red River and Mekong deltas hydrogeological models. They are developed using MODFLOW, with a prior geological model constructed using ArchPy, an open-source method and Python module for modelling heterogeneous Quaternary environments. ArchPy allows stochastic modelling, a semi-automated workflow and a flexible, all-in-one framework. The land-ocean transition zone is represented with an equivalent freshwater head boundary at this stage of model development, in order to ensure reasonable computing times for inversion calibration.