The crystal structure of alkali/water-poor beryl (H2O + Na2O + Cs2O < 1.2 wt%) was reinvestigated by means of laser ablation inductively coupled plasma mass spectroscopy, thermogravimetric analysis, neutron diffraction, and polarized infrared spectroscopy to determine the real topological configuration of the extra-framework content in the six-membered ring channels. Analysis of the nuclear density Fourier map suggests that the (water) oxygen is located along the sixfold axis at the 2a site (0,0,1/4), whereas the (water) protons are at −0.028(7), −0.071(3), 0.332(1). The hydrogen atoms are distributed in 6 × 2 equivalent positions, above and below the oxygen site. Geometrical configuration of the water molecule is well defined: the O-H bond distance is 0.949(18) Å and the H-O-H bond angle is 106.9(2.2)°. The H···H vector is oriented at ~4° from . This configuration is completely different from that found in alkali-rich beryl, where the H···H vector is perpendicular to . Na is probably located, with the H2O oxygen, at the 2a site. According to the chemical analysis, which shows that the amounts of other alkali and earth-alkali cations are negligible (Rb, K, Mg, Mn ≤ 110 ppm, Ca ≤ 225 ppm, Cs ≤ 430 ppm), no effect of other cations on the extra-framework population was observed in the structural refinement. The final agreement index (R1) of the structural refinement was 0.037 for 34 refined parameters and 160 unique reflections with Fo > 4σ(Fo). The topological configuration of the H2O molecule into the channel is confirmed by the spectroscopic investigation. Polarized single-crystal IR spectra show that the H2O molecule is oriented with the molecular symmetry axis perpendicular to the hexagonal axis and H···H vector parallel (or quasi-parallel) to .