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Groundwater is a vital resource for socio-economic sustainability ye is increasingly threatened by climate change and rising anthropogenic pressures. Lebanon, and particularly the Al Assi River Basin (ARB), experiences recurrent droughts, but limited meteorological and groundwater observations hinder effective water resources monitoring and management. This study employs satellite-derived datasets to investigate the relationship between hydrological and hydrogeological drought indicators across Lebanon, with emphasis on the ARB. The Standardized Precipitation Index (SPI) and the Standardized Precipitation and Evapotranspiration Index (SPEI) were computed from CHIRPS precipitation and CHIRTS-ERA5 temperature data at multiple accumulation periods. Groundwater drought was quantified using the Groundwater Drought Index (GGDI), derived from GRACE terrestrial water storage anomalies. SPI, SPEI, and GGDI were harmonized at a 10 km resolution, and correlation analyses, including lagged correlations, were conducted to examine their temporal relationship. Results show that SPEI at 18-month accumulation exhibits the highest correlation with GGDI (R ≈ 0.70) at zero lag, reflecting the response of the multi-layered ARB aquifer system. Future SPEI projections were derived using bias-corrected outputs from the CNRM-ALADIN53 regional climate model under RCP 4.5 and RCP 8.5 scenarios. Using the regression model resulting from the strongest correlation, future GGDI projections were generated, highlighting a progressive increase in drought-affected areas, with the most severe groundwater deficits expected under RCP 8.5 by the late 21st century. These findings underscore the need for integrated water-resource management that combines climate-informed planning, satellite-based monitoring, and strengthened in-situ hydrogeological networks to improve resilience to future climatic extremes in data-scarce regions. This study assesses how meteorological drought propagates into groundwater systems under climate change in data-scarce Mediterranean regions, with a specific focus on Lebanon and the Al Assi River Basin. The analysis integrates satellite-derived precipitation (CHIRPS), temperature (CHIRTS-ERA5), and GRACE-based terrestrial water storage anomalies to overcome the absence of in-situ hydrometeorological and groundwater records. Meteorological drought indices (SPI and SPEI) were computed at multiple accumulation periods, while the GRACE-derived Groundwater Drought Index (GGDI) was used to characterize hydrogeological drought conditions. Correlation analyses were conducted to identify the most robust proxy for groundwater drought, revealing that SPEI-18 displays the strongest spatial and temporal correspondence with GGDI, reaching up to 97% high-correlation coverage in the ARB at zero lag. Bias-corrected climate projections from the CNRM-ALADIN53 regional model (RCP 4.5 and RCP 8.5) were used to generate future SPEI-18 and GGDI scenarios for three-time horizons (2030–2050, 2060–2080, 2080–2100). Results show a progressive intensification of both meteorological and groundwater drought throughout the 21st century, with the most severe declines projected under RCP 8.5. Drought-affected areas expand substantially, while groundwater drought classes shift toward higher frequency and severity. The findings underscore that satellite-based indicators offer a reliable framework for monitoring groundwater stress where observational networks are limited. Moreover, the study highlights the urgent need for integrated, climate-responsive water-resource management strategies to safeguard long-term water security in Lebanon and similar data-limited Mediterranean basins. Satellite data and drought indices enable robust climate–water assessment in data-scarce regions. GRACE-based groundwater drought index captures cumulative water-mass changes in Lebanon’s multi-layered aquifers. In ARB, SPEI-18 shows the strongest correlation with groundwater drought, reflecting long-term aquifer responses. Future climate projections indicate up to 2.1 °C warming and 14% precipitation decline by 2100.