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Accurately assessing groundwater storage changes in Niger is critical for long-term water resource management but is difficult due to sparse field data. We present a study of groundwater storage changes and recharge in Southern Niger, computed using data from NASA Gravity Recovery and Climate Experiment (GRACE) mission. We compute a groundwater storage anomaly estimate by subtracting the surface water anomaly provided by the Global Land Data Assimilation System (GLDAS) model from the GRACE total water storage anomaly. We use a statistical model to fill gaps in the GRACE data. We analyze the time period from 2002 to 2021, which corresponds to the life span of the GRACE mission, and show that there is little change in groundwater storage from 2002–2010, but a steep rise in storage from 2010–2021, which can partially be explained by a period of increased precipitation. We use the Water Table Fluctuation method to estimate recharge rates over this period and compare these values with previous estimates. We show that for the time range analyzed, groundwater resources in Niger are not being overutilized and could be further developed for beneficial use. Our estimated recharge rates compare favorably to previous estimates and provide managers with the data required to understand how much additional water could be extracted in a sustainable manner.