Some of the most outstanding hypogenic gypsum speleothems worldwide have been recently discovered in the Naica mines. The Cueva de las Espadas (Swords Cave), which lies at 120 m depth, hosts a rare type of speleothem called “espada” (“sword”). This study contributes to the understanding of the mineralogical composition of these singular speleothems, by means of their examination using micro-Raman spectroscopy, FT-IR spectroscopy and EDX microprobe. Our data revealed a complex mineralogy comprising a high-purity selenite core covered by several layers of calcite, aragonite and gypsum. Solid inclusions of polymetallic oxides (Mn-Pb-Zn) and graphite were also detected. The position of the water table during the genesis of the “espada” speleothems (over the past 60 kyr) was deduced from their mineralogy. Water level fluctuations at around -120 m depth led to environmental changes within the Cueva de las Espadas. The selenite core and gypsum layers were precipitated under biphasic (water-rock) conditions when the cave was submerged under hydrothermal water. The aragonite precipitation required triphasic (air-water-rock) conditions and occurred when the water table intercepted the cave, allowing the CO2 exchange necessary for carbonate precipitation. Solid inclusions were trapped in an aerobic environment when the gypsum-aragonite boundary condition occurred. A thin calcite layer was precipitated under vadose conditions after the water table definitively moved out of the cave.