We present a high-resolution conceptual hydrogeological model for complex basaltic volcanic islands based on Mayotte Island in the Comoros. Its geological structure and hydrogeological functioning are deduced from a large dataset: geological mapping, geophysics, some forty new boreholes, piezometric data, hydraulic conductivity, hydrochemical data, etc. We describe previously unknown deep cut-and-fill palaeovalleys. The resulting conceptual geological and hydrogeological model of the island is very different from the Hawaiian model, in that it lacks a low-elevation basal aquifer and dyke-impounded high-level aquifers. It is closer to the Canary Islands model, which has, however, not yet been described at a high-resolution scale. It does not have a continuous aquifer, but rather a discontinuous succession of perched aquifers separated by aquicludes and aquitards. This results more from the complex geological structure of the island, which has experienced several phases of volcanism, erosion and weathering, than from its age, but is also a result of the high-resolution scale of the model. High-resolution conceptual modelling is now necessary to solve problems of applied geology and hydrogeology.