The coastal basin of Benin covers 12377 km² of the transboundary aquifer system shared by Benin, Nigeria and Togo. Groundwater is the mean water supply source of a population approximately estimated by 4 million inhabitants. Population rapid growth with the rate of 4.5% induces extension of human settlements which interaction with climate variability affect groundwater quality. Statistical analyses were used to highlight observed climate change. Seasonal analysis of 40 shallow and deep wells, boreholes and spring water sampling and land use land cover (data provided by LANDSAT ETM7+, MSS, and SPOT imagery for 1973, 1995 and 2005) diachronic analysis helped to emphasise environmental change impacts on groundwater quality. Furthermore, binary diagram method was used to interpreted geochemical process of water mineralization. Water quality is also appreciated from the drinking water quality standards of WHO. This study shows that groundwater mineralization is dominated by calcium, sodium, bicarbonates, nitrogen and chloride depending on ions exchange process in the wet or dry period. Bacterial polluting agents were numerous (total coliforms, Escherichia coli (in dry period) and fecal streptococcus (in wet period)). On the whole, depth of aquifers, land use, unhealthiness around the water supply sources, induced recharge from inadequate sanitation facilities and sea water intrusion interaction with hydroclimatic change are the mean factors of the strong deterioration of groundwater. Groundwater quality assessment could contribute to plan transboundary aquifers management based on local hydrogeological basin scale.