In this research, we characterized the changes in Gravity Recovery and Climate Experiment’s (GRACE) monthly total water storage anomaly (TWSA) in 18 surface basins and 12 principal aquifers in the Conterminous United States (CONUS) over 2003–2016. Regions with high variability in storage were identified. Ten basins and 4 aquifers showed significant change in storage. Eight surface basins and 8 aquifers were found to show decadal stability in storage. A pixel-based analysis of storage showed that New England basin and North Atlantic Coastal Plain aquifer showed the largest area under positive storage change. Whereas, the Lower Colorado basin and California aquifers showed largest area under negative change. This study found that historically wetter regions (with more storage) are becoming wetter and dryer regions (with less storage) are becoming dryer. Fourier analysis of the GRACE data showed that while all basins exhibited prominent annual periodicities, significant sub-annual and multi-annual cycles also exist in some basins. The storage turnover period was estimated to range between 6 to 12 months. The primary explanatory variable (PEV) of TWSA was identified for each region. This study provides new insights on several aspects of basin or aquifer storage that are important for understanding basin/aquifer hydrology.