The crystal structure of beryl has been refined from single-crystal neutron and X-ray data obtained on two samples with different alkali and H2O contents [morganite: Al2Be2.65Li0.32Si6O18.(Na0.22Cs0.080.54H2O); aquamarine: Al1.94Fe0.06Be3Si6O18. (Na0.020.28H2O)] in order to elucidate the ambiguities affecting the assignment of atomic species to the channel sites. Neutron data for morganite were obtained at 295 and 30 K; neutron data for aquamarine and X-ray data for both samples were obtained at room temperature. Final agreement factors for the three neutron and the two X-ray refinements are in the order [R(unweighted)] 0.034, 0.052, 0.033, 0.023, 0.022. The expected Li substitutions in the Be tetrahedral site and of Fe in the Al octahedral site were clearly confirmed by the neutron data refinements. Accurate site occupancy refinements in the 2a and 2b channel sites at 0,0, 1/4 and 0,0,0, obtained also through location of the H atoms, yielded two distinct configurations with Cs and H2O at 0,0,1/4 and Na at 0,0,0 in morganite, and Na and H2O at 0,0,1/4 in aquamarine (with 2b empty). The H2O molecules attain two distinct orientations in the two samples with H-H vectors on the ab plane in morganite and parallel to the c axis in aquamarine. The H2O orientations are in agreement with type II H2O being present in alkali-containing beryl, and type I H2O being present in alkali-free samples, as found by spectroscopic investigations.