A conceptual hydrogeological model of the Mio-Pleistocene deposits in the Almada region, located in the Cenozoic aquifer system of the Lower Tagus Basin (Portugal), has been developed. Though numerous studies have been conducted on its geological features, there have not been enough hydrogeological investigations to define the origin, flow path and the groundwater quality and to understand the coexistence of overlapped interacting aquifers. Therefore, a study is presented here on the occurrences and features of groundwater resources in the Almada region based on an inventory in the field (wells, springs and boreholes), physical and chemical analyses, geologic setting, and tectonic and geomorphologic observations. This aquifer system has long been a source of concern because of the high level of extraction over the last few decades, as well as the progressive degradation of the water quality. Available groundwater resources have been affected by intensive agricultural and industrial activity, as a consequence of incorrect or non-existent hydrogeological knowledge.