A known deterrent to the large-scale development and use of cellulose nanocrystals (CNCs) in composite materials is their affinity for moisture, which has a profound effect on dispersion, wetting, interfacial adhesion, matrix crystallization, water uptake, and hydrothermal stability. To quantify and control the hydration and confinement of absorbed water in CNCs, we studied sulfated-CNCs neutralized with sodium cations and CNCs functionalized with less hydrophilic methyl(triphenyl)phosphonium cations. Films were cast from water suspensions at 20 °C under controlled humidity and drying rate, yielding CNC materials with distinguishably different dielectric properties and cholesteric structures. By controlling the evaporation rate, we obtained self-assembled chiral CNC films with extended uniformity, having helical modulation length (nominal pitch) tunable from 1300 to 600 nm. SEM imaging and UV–vis–NIR total reflectance spectra revealed tighter and more uniform CNC packing in films cast at slow evaporation rates or having lower surface energy when modified with phosphonium. The dielectric constant was measured by a noncontact microwave cavity perturbation method and fitted to a classical mixing model employing randomly oriented ellipsoidal water inclusions. The dielectric constant of absorbed water was found to be significantly smaller than that for free liquid indicating a limited mobility due to binding with the CNC “matrix”. In the case of hydrophilic Na-modified CNCs, a decreasing pitch led to greater anisotropy in the shape of moisture inclusions (ellipsoidal to platelet-like) and greater confinement. In contrast, the structure of hydrophobic phosphonium-modified CNC films was found to have reduced pitch, yet the shape of confined water remained predominantly spherical. These results provide a useful perspective on the current state of understanding of CNC–water interactions as well as on CNC self-assembly mechanisms. More broadly, we believe that our results are beneficial for the realization of CNC-based functional materials and composites.