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The estimation of groundwater storage variations is important for quantifying available water resources and managing storage surpluses to alleviate storage deficiencies during droughts. This is particularly true in semi-arid regions, where multiyear droughts can be common. To complement the local information provided by soil moisture and well level measurements, land models such as the Community Land Model (CLM) can be used to simulate regional scale water storage variations. CLM includes a bulk aquifer model to simulate saturated water storage dynamics below the model soil column. Aquifer storage increases when it receives recharge from the overlying soil column, and decreases due to lateral flow (i.e., base flow) and capillary rise. In this study, we examine the response of the CLM aquifer model to transitions between low and high recharge inputs, and show that the model simulates unrealistic long-period behavior relative to total water storage (TWS) observations from the Gravity Recovery and Climate Experiment (GRACE). We attribute the model’s poor response to large wetting events to the lack of a finite lower boundary in the bulk aquifer model. We show that by removing the bulk aquifer model and adding a zero-flux boundary condition at the base of the soil column, good agreement with GRACE observations can be achieved. In addition, we examine the sensitivity of simulated total water storage to the depth at which the zero-flux boundary is applied, i.e., the thickness of the soil column. Based on comparisons to GRACE, an optimal soil thickness map is constructed. Simulations using the modified CLM with the derived soil thickness map are shown to perform as well or better than standard CLM simulations. The improvements in simulated, climatically induced, long-period water storage variability will reduce the uncertainty in GRACE-based estimates of anthropogenic groundwater depletion.