Along the West-African coast, groundwater is under several threats coming from both human activities and climate change. However, hydrogeological studies have so far been conducted in a piecemeal way, city by city. In this paper, a regional study was conducted along the Beninese coast, combining hydrogeochemistry and water stable isotopes. Monthly rainfall samples were analyzed in terms of chemistry and isotopes as well as groundwater from Holocene (upper aquifer) and Mio-Plio-Pleistocene (lower aquifer). This allowed to determine the recharge timing of aquifers (April to October, excluding August). Rainwater then infiltrates the soil with a slight evaporation. The upper aquifer, more heterogeneous, is displaying many different water types while the lower aquifer shows mainly a Na-Cl water type. While the upper aquifer shows many signs of contamination from human activities and saltwater intrusion from lakes and lagoons, the deeper aquifer is more influenced by a geogenic signature. These results are then interpreted regarding the demographic trends and climate change scenario. In the long-term, the groundwater level of the lower aquifer is expected to decrease as the rate of abstraction increases and recharge rate decreases. It is therefore recommended to develop adapted and urgent protection measures of the water resource to ensure sustainable and healthy groundwater exploitation.