Ammonium-illite (NH4-I) is one of the alteration products present in a breccia structure in the fossil hydrothermal system from Harghita Bãi (East Carpathians), Romania. A series from smectite (S) via ordered interstratified structures to NH4-I (40 to 5%S) was characterized by X-ray diffraction (XRD), Fourier transform-infrared spectroscopy (FTIR), scanning and transmission electron microscopy (SEM and TEM), and chemical analyses. Calculation of one-dimensional X-ray patterns was simulated with the NEWMOD code. Transition from two- to one-water smectite interlayer was identified by XRD. Selected samples were saturated with K+-, Mg2+-, and Li+-cations to differentiate low- to high-charge smectite or beidelite layers. X-ray patterns of random powders of K+-saturated samples, heated at 300 °C show a transition from 1Md to cis- and trans-vacant 1M polytype. The cell parameters of the cis-vacant and trans-vacant 1M polytype were calculated by oblique texture electron diffraction. The vibration frequencies at 1430 cm−1 of the N-H bond were identified in the samples analyzed. Scanning and transmission electron microscopy images show morphological changes from flaky to lath-like shapes. The mean shape ratio of lath crystals ranges from 6 to 5.42 nm and the mean area from 7.8 to 24 × 104 nm2. The mean thickness of the NH4-I layers ranges from 4.62 to 7.89 nm. The calculated structural formula of end-member NH4-I (5%S) is: [(NH4+)0.66K0.10+Na0.01+Sr0.022+]0.81 (Al1.853+Fe0.013+Mg0.152+)2.01(Si3.304+ Al0.703+)4.00O10(OH)2. The fixed NH4+ content quantified ranges from 0.39 to 0.66 atoms per half unit cell [O10(OH)2]. Tetrahedral and octahedral substitutions took place as the %S decreases. The NH4-I-S series formed via direct precipitation from solution at different temperatures.