Study regionFractured aquifers in Benin have emerged in the past decades as a critical resource because of the increasing domestic water needs, agriculture, and livestock breeding. Hence this study was undertaken in the poorly gauged and complex basement aquifers beneath the 9th latitude. Study focusTo aid water resources management and sustainability, this study combined satellite remote sensing products with outputs from hydrological models and in situ measurement to assess the spatial and temporal patterns of water storage changes, including groundwater. The fractured aquifers’ hydrogeological regime is further analysed through monitoring wells’ series interpretation. New hydrological insights for the regionResults show considerable inter-annual variations in Terrestrial Water Storage (TWS) during the study period (2003–2019). Two uptrend intervals characterized by wet hydrological seasons from 2006 to 2013 and 2016–2019 with respectively, Sen’s slope values of 1.16 mm/yr and 4.47 mm/yr were observed. However, two downtrend intervals represented by dry hydrological seasons with Sen’s slopes of − 1.01 mm/yr (2003–2006) and − 1.19 mm/yr (2013–2016) were also observed. The inter-annual seasonality in land water storage components showed that unlike the 4 climatic seasons, the hydrogeological regime is affected by 3 seasons each year. The first dry season takes place from January to April-May (−29.1 ± 17.7 mm/yr) followed by the wet season (April-May to October-November: 41.6 ± 26.4 mm/yr) and the last dry period, which is stronger (November to December: −53.7 ± 31.6 mm/yr). Soil moisture (SM) and canopy water content (CW) declined during the 2008–2016 period, coinciding with decline in Tree cover areas, which dropped by 25.5% (3086.7 sqkm). Further from 2007 to 2014, the four monitoring wells have seen the groundwater level increased by, 1.44 m/yr, 2.0 m/yr, 3.2 m/yr, and 0.56 m/yr for the Affon, Zou, Okpara and Couffo sub-basins, respectively. The retrieved TWS and Water ‐ Global Assessment and Prognosis groundwater storage (WaterGap-GWS) sub-domains based on statistical decomposition was used to identify hidden patterns to improve knowledge on the climatic and hydrological conditions, which affected land water storage. Moreover, TWS, GWS and SM lost water 51%, 57% and 47% of the time, respectively, during the period and the storage potential is lower for the aquifers compared to the unsaturated zone. Precipitation is recognized as a primary driver of GWS (r = 0.69; α = 0.05) in the region and a change in GWS is more likely to drive the CW and affect the vegetation greenness. Moreover, the anthropogenic pressure exacerbates Tree cover loss. Additionally, the Extra Tree regressor performs best in the groundwater storage change ∆GWS prediction with a strong and positive Pearson Correlation Coefficient of 0.92. The basement aquifers assessment using the aforementioned approach has potential to support large-scale monitoring efforts for more reliable water resources management in the region.