Groundwater is a crucial resource for ecosystems, agriculture, and human settlements worldwide, which is the subject of our study. This study meticulously evaluates the spatial and temporal variations in groundwater sustainability across distinct climatic regions of Nigeria. The methodology involves using the Groundwater Storage (GWS) data from the Global Land Data Assimilation System (GLDAS) to calculate Reliability, Resilience, and Vulnerability (RRV) indices for estimating groundwater sustainability. The modified Mann-Kendall (MMK) and Sen's Slope methods are used to detect trends in groundwater sustainability over two decades (2003–2023). The drivers of groundwater sustainability changes are identified utilizing Climate Research Unit (CRU) rainfall, potential evapotranspiration (PET) data, and gridded groundwater irrigation data. The results reveal critical regional disparities in GWS and a concerning southward decrease in sustainability. The northern regions exhibit a decline in vulnerability by −0.4 to −0.1 per decade, increasing reliability by 0.35–0.40 per decade and resilience by 0.05–0.1 per decade. These caused an increase in groundwater sustainability ranging from 0.05 to 0.15 per decade in the north, while a decline by −0.005 to 0 per decade in other areas. Rainfall shows positive correlations up to +0.6 with sustainability, while PET shows correlations between −0.3 and −0.6 with sustainability. The results suggest that decreased rainfall and increased PET cause decreased groundwater sustainability in the south. This work underscores the practical need for tailored, region-specific groundwater management practices in Nigeria.