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Speleothems frequently host “fossil” fluids that were trapped in small inclusions during growth. Such fluids may provide valuable clues to past microbial, geochemical, and climatic processes during their formation. However, one difficulty is to understand which gases represent background atmosphere and fluids within a given cave system at a particular time, and which may be the product of post-trapping residual microbial activity or abiotic chemical reactions? Do we have any hope of sorting out these differences? The success depends on a quantitative understanding of the gas composition trapped in the inclusions and an understanding of the interactions of cave mineralogy, air and water chemistry, and microbiological processes that may interfere with climatic or geochemical interpretations. Our proof-of-concept project uses time synchronous samples from several sites. We report here on this pilot investigation of speleothem inclusions using a methodology for quantitatively analyzing gases dissolved in inclusion fluids. We use incremental crushing of highly spatially resolved samples by mass spectrometry. Here, we report primarily on CH4, CO2, O2, and N2, but have included other detectable gases. The detection limit for He within aqueous fluid inclusions is ~0.2 ppm and gas ratios have ~5% precision using natural standards. We used chemically inert argon as a tracer gas to normalize results to air or air saturated water. This enables interpretation of gas data despite variability in hydrological and geological cave histories. Results are variable. For example, in one case oxygen was depleted while nitrogen was increased, which may be attributable to the breakdown of nitrate or nitrogen-containing biomolecules. In other cases, oxygen is enriched which may be attributed to several factors both geochemical and biological. We suggest potential interpretations between the competing hypotheses with larger future data sets. This first attempt tackles the complex and intertwined speleological questions using the inclusion gas method.