Management of coastal groundwater must take account of the complex hydrological processes and uncertainties associated with this environment. Regular evaluation of mechanisms, parameters and boundary conditions is required to understand groundwater flow and to develop a robust conceptual model. In certain conditions, as in tropical regions, due to the high intensity and variability of natural drivers (precipitation, evapotranspiration), a comprehensive hydrogeological characterization may be needed. Data on transient recharge, tide-driven fluctuations of groundwater receptors (seas, rivers) and the activation status of drainage networks may need to be updated recurrently, as they likely influence groundwater balance. Numerical models are applied at various phases of a hydrogeological investigation to elucidate preliminary conceptual models and to guide the field characterization. Those models provide a quantitative framework for synthesizing field information and verifying mechanisms readily contributing to a cost-effective decision-making process. This article presents a systematic hydrogeological characterization of a coastal basin in a tropical region of southern Brazil that is affected by intensive precipitation and ocean tides; precipitation is the main process driving groundwater flow, although head variations at the boundaries affect a spatiotemporal distribution of the water table. A set of numerical experiments is deployed to test the understanding of natural processes and to assist additional field campaigns. The hierarchy of hydrogeological processes is evaluated over different scales, to eliminate less sensitive mechanisms. By presenting the detailed setup information on model development, the applications are demonstrated and limitations are discussed in light of the available field data and specific research objectives.