Palygorskite is a Mg-rich fibrous clay, present in nature as a mixture of two intricately intertwined polymorphs – monoclinic (C2/m) and orthorhombic (Pbmn) – characterized by the presence of channels along Z-axis, filled by weakly bound zeolitic water. A neutron powder diffraction study was carried out by full Rietveld refinement on a deuterated sample, measured at ISIS on the HRPD beam-line. The positions of oxygen and deuterium atoms of the zeolitic water were located ab initio through cyclically repeated Difference Fourier maps, and their atomic coordinates and occupancy factors were refined. The frameworks of both monoclinic and orthorhombic palygorskite do not differ significantly from the models reported in the literature, although they are more distorted. The arrangement of the zeolitic water molecules is highly disordered and different in the two polymorphs. Given the coexistence of several deuterium sets, two different H-bonding schemes are proposed for each polymorph. Further H-bonding alternatives could be derived by considering the location of oxygen atoms in partially occupied symmetry related sites. The links between the zeolitic water and the clay framework appear to be weaker in orthorhombic than in monoclinic palygorskite, as shown by the lower number and different strength of H-bonds. The detailed knowledge of the zeolitic water arrangement may help in better understanding the structural features and production techniques of palygorskite-based compounds of great interest, such as the Maya Blue pigment.