The Thunder Bay Amethyst Mine exploits a vein system in which the main zoned sequence consists of chalcedony, colorless quartz, and three to four stages of amethyst. The main sequence surrounds fragments of a brecciated earlier sequence containing chalcedony, colorless quartz, and prasiolite, which appears to be thermally bleached amethyst. The vein system occupies a fault in Archean granodiorite and is associated with a narrow zone of chloritic and hematite alteration overprinted by weak argillic alteration. Fragments of Proterozoic (1339 Ma) Sibley Group rocks occur in the vein system, indicating the former presence of a shallow cover during deposition of quartz and limiting the maximum age of the deposit. These downfallen fragments and the abundance of vugs indicate near-surface formation of the deposit.Main-stage fluid-inclusion homogenization temperatures are in the range from 91.2 to 40.9 °C (mean 68.4 °C) in amethyst, whereas in colorless quartz homogenization temperatures range from 146.5 to 114.7 °C (mean 132.1 °C). Eutectic temperatures fall in three ranges with means of −50.9, −48.7, and −43.9 °C, which are related to paragenetic position and indicate an NaCl–CaCl2–H2O system, with possible additional components in later inclusions. Salinities in amethyst-hosted inclusions decrease in the growth direction from 22.9 to 15.3 equiv.wt% NaCl.Trace sulfide and other mineral inclusions indicate a trend of decreasing Eh and pH from an initially rather oxidized (sulfate stable) to a reduced (sulfide stable) condition during deposition. Sulfur isotopic composition in pyrite and chalcopyrite ranges from δ34S = −0.4 to −1.4‰ and is similar to values obtained from lead–zinc–barite in other vein deposits surrounding the Sibley depositional basin. Oxygen isotopes in quartz range from δ18O = +12.7 to +17.1‰, corresponding to δ18O(H2O) = −2.1 to −12.8‰ using fluid-inclusion temperatures. Fresh quartz monzonite wall rock (δ18O = +11.82‰) and altered quartz monzonite (δ18O = +11.01‰) do not seem to have undergone significant isotopic exchange with the hydrothermal solution, and the trend of isotopic change does not account for the trend of δ18O(H2O) determined in quartz. Rather, mixing of local meteoric water with a basinal brine appears to explain the observed trend.The amethyst deposits are believed to have been formed by basinal brines expelled from Sibley Group sediments. The brines dissolved silica by alteration processes accompanying their passage through granitic basement rocks in basin marginal faults. Amethyst was deposited on mixing with meteoric water. The temperature interval for amethyst formation appears to be restricted to less than ~90 °C. Temperatures causing thermal bleaching of amethyst are as low as 145 °C, and possibly 115 °C, as indicated by these results. This low range of temperature is not in agreement with bench-type experiments indicating bleaching at hundreds of degrees Celsius.