Layered silicates have important applications as host materials, supports for catalysis, and zeolite precursors. However, their local structures are often challenging to establish due to disorder of the sheet assemblies. We present a new protocol that combines long- and short-range structural constraints from diffraction and solid-state NMR techniques, respectively, to determine the molecular structure of layered silicates in the presence of various extents of stacking disorder. Solid-state 29Si NMR data are largely insensitive to the incomplete extent of three-dimensional (3D) crystallinity that limits the interpretation of diffraction data alone to the identification of possible unit cells and space groups. State-of-the-art NMR crystallography techniques consequently provide a simplified view of materials from which candidate framework structures can be built and evaluated based on local structural constraints, including interatomic distances, Si site numbers and multiplicities, and Si–O–Si connectivities, and refined using density functional theory. This protocol was applied to a new layered silicate material named CLS-1, of composition [Si5O11H][C9N2H15]·1.9(H2O), synthesized by using a fluoride-based protocol and cationic alkylaminopyridinium as a structure-directing agent (SDA). Despite the intrinsic complexity and partial ordering of the intersheet arrangements and organic–inorganic interactions, this led to the identification of a single space group that is compatible with both NMR and diffraction data, from which the silicate framework structure could be established,. The remarkable similarities between the layered framework structures of CLS-1, HUS-2 (Tsunoji et al. J. Mater. Chem. 2012, 22, 13682), and another layered silicate material with a radically different morphology and extent of stacking order and interlayer dynamics, established by using a similar approach (Brouwer et al. J. Am. Chem. Soc. 2013, 135, 5641), point to the remarkable robustness of this previously unknown silicate framework type.