This work analyzes the geological evolution of sedimentary deposits in the coastal aquifer of Garopaba, south Brazil, using ground penetrating radar (GPR) and data from tubular wells. The aquifer is localized in the coastal plain, where Quaternary lagoon-barrier environments are set between the Precambrian crystalline mountains and the sea. Over ten tubular wells are scattered in urbanized areas, which highlights the vulnerability of the unconfined, granular shallow aquifer. The results show that the aquifer has lithologic units of local scale. Tubular well data show the basal limit of the aquifer overlying clayey layers between 30 and 40 m deep and intercalation of sand layers up to the surface, mostly fine to very fine sand, with metric thickness, secondary lenses of clay and minor occurrence of gravel. The radarfacies interpretation shows fluvial-estuarine deposits as a local hydrostratigraphic unit, with lateral accretion bars filling a NE-axis paleochannel. The basal surface of the channel is interpreted as the sequence boundary surface of the lagoon-barrier systems III (upper Pleistocene) and IV (Holocene). The geological evolution of the aquifer is related to the upper Pleistocene marine regression (120–18 ka), that caused the aerial exposure of the continental shelf, and the development of complex drainage channels, which were superimposed during the Holocene transgression by lagoon-barrier IV deposits. After the post-glacial transgression, the lowering of the RSL to the current level promoted the silting of part of the lagoon system by continental sedimentation and aeolian deposits composing the surface.