This study aims at establishing a groundwater model for the 100-meter aquifer of a coastal area of the Mekong Delta, and applying it to simulation of the groundwater heads under possible changes in rainfall and groundwater management in the future. The model, iMOD, was calibrated using historical data of groundwater level and model input requirements. It was confirmed that the calibrated model could work properly to reproduce the distribution of the groundwater table and its response. For scenario setting, several cases of future rainfall conditions for the period from 2015 to 2035 were set up based on the downscaled output from the global climate model with bias correction. For each of the combinations of climatic conditions and pumpage, model simulation was carried out to estimate groundwater tables. The results showed: (1) If the groundwater pumping stays at the same level as present, groundwater heads can maintain the present level under increased recharge from the future rainfall, whereas slight decline in groundwater heads would continue under the current rainfall; (2) If the groundwater pumping increases along with increasing water demand, significant consecutive drawdown of groundwater tables will happen. Particularly when considering some reduction in recharge due to rainfall loss and uncertainty of rainfall, groundwater depletion might be more serious; (3) Reduction in pumping rate was found to contribute much for recovery of groundwater.