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Application of novel proxies, such as the stable isotope compositions and noble gas concentrations of fossil drip water trapped as inclusions in stalagmites, have the potential to provide unique constraints on past hydroclimate states and surface temperatures. Geochemical analysis of inclusion waters, however, requires an understanding of the three‐dimensional spatial distribution of dominantly liquid‐ versus air‐filled inclusions in a given stalagmite. Here we couple neutron computed tomography and medium‐ to high‐resolution X‐ray computed tomography to map out the three‐dimensional calcite density and distribution of liquid‐ versus air‐filled inclusions within a Sierra Nevada stalagmite (ML‐1), which formed during the last deglaciation (18.5 to 11.7 ka). Comparison of coupled neutron computed tomography‐X‐ray computed tomography results with a time series of stalagmite calcite fabrics indicates that although highest density calcite contains abundant liquid (fluid)‐filled inclusions, calcite density and fabric overall were secondary controls on the liquid inclusion distribution (LID). Furthermore, a multistatistical evaluation of the stalagmite time series indicates a significant relationship at the multicentury‐ to millennial‐scale between LID and calcite δ¹⁸O and δ¹³C that suggests a potential link between LID and water availability to the cave.