In this work, we studied the hydrothermal agates from the Neogene–Quaternary volcanic district of Allumiere-Tolfa, north-west of Rome (Latium, Italy) using a combination of micro-textural, spectroscopic, and geochemical data. The examined sample consists of (1) an outer cristobalite layer deposited during the early stages of growth, (2) a sequence of chalcedonic bands (including i.e., length-fast, zebraic, and minor length-slow chalcedony) with variable moganite content (up to ca. 48 wt%), (3) an inner layer of terminated hyaline quartz crystals. The textures of the various SiO2 phases and their trace element content (Al, Li, B, Ti, Ga, Ge, As), as well as the presence of mineral inclusions (i.e., Fe-oxides and sulfates), is the result of physicochemical fluctuations of SiO2-bearing fluids. Positive correlation between Al and Li, low Al/Li ratio, and low Ti in hyaline quartz points to low-temperature hydrothermal environment. Local enrichment of B and As in chalcedony-rich layers are attributed to pH fluctuations. Analysis of the FT-IR spectra in the principal OH-stretching region (2750–3750 cm−1) shows that the silanol and molecular water signals are directly proportional. Strikingly, combined Raman and FT-IR spectroscopy on the chalcedonic bands reveals an anticorrelation between the moganite content and total water (SiOH + molH2O) signal. The moganite content is compatible with magmatic-hydrothermal sulfate/alkaline fluids at a temperature of 100–200 °C, whereas the boron-rich chalcedony can be favored by neutral/acidic conditions. The final Bambauer quartz growth lamellae testifies diluted SiO2-bearing solutions at lower temperature. These findings suggest a genetic scenario dominated by pH fluctuations in the circulating hydrothermal fluid.