Accurate and densely covered specific yields (Sy) are essential for estimating the storage capacity of a groundwater reservoir. A cross-well pumping test can determine Sy, but its high cost often makes it unsuitable for sampling high-resolution Sy. The gravity-based method (GBM) based on gravity changes near existing groundwater wells may outperform cross-well pumping tests in estimating Sy. We established 10 gravity sites close to groundwater wells in the aquifer-rich Choushui River Alluvial Fan and Mingchu Basin in central Taiwan and measured gravity changes with two FG5 gravimeters from 2012 to 2017. Thirty-nine Sy values with formal errors are determined by natural rises and falls in gravity and groundwater level. The representative Sy values (0.04 to 0.29) from GBM are in general consistent with those from cross-well pumping tests (0.03 to 0.24). Repeated groundwater level changes over similar depth range at different times serve as revisit tests, showing that GBM can reproduce a reliable Sy value at a given site and depth. Soil moisture and compaction data show that the effects of gravity changes originating from unsaturated zones and deep aquifer layers are minor. Using the cylinder model for aquifers with limited lateral extents, we assess the validity of the Bouguer model by quantifying gravity differences and relative Sy differences originating from the model assumption. Improvements in environmental resilience and transportability achieved by recent atomic gravimeters may increase the potential of GBM to replace or supplement cross-well pumping tests in densifying Sy point densities for an improved groundwater resource management.