In 2016–17 much of East Africa was affected by a severe drought which has been attributed to Indian Ocean Dipole and El Niño Southern Oscillation conditions. Extreme events such as this have immediate and knock-on effects on water availability for household, agricultural and industrial use. Groundwater resources can provide a buffer in times of drought, but may themselves be stressed by reduced recharge and increased usage, posing significant challenges to groundwater resource management. In the context of East Africa, groundwater management is also hampered by a lack of information on aquifer characteristics. With the aim of addressing this knowledge gap, this study shows the hydrogeological behaviour before and during La Niña 2016/17 drought in southern coastal Kenya on a groundwater system which sits within a geological structure which is representative of an important portion of the East African coast. Diverse hydrochemical and isotopic campaigns, as well as groundwater head variation measurements, were carried out to study the groundwater hydrodynamics and thus characterize the aquifer system under climatic conditions before and during the La Niña event. This information is complemented with an estimation of changes in local recharge since 2012 using local data sets. The main consequence of the drought was a 69% reduction of recharge compared to an average climatic year. There was reduced recharge during the first rainy season (April–June) and no recharge during the second wet season (October–December). There was a concurrent increase in seawater intrusion even during the wet season.