Different forms of abundant silica (e.g., quartz and chalcedony) are closely associated with many types of ore deposits in igneous, metamorphic, and sedimentary environments. Occurrence of quartz and metal-bearing minerals together strongly indicates that silica is an important component in hydrothermal fluids transporting and concentrating economic metals to the ore grade, however chemical and physical characteristics of such ore-forming media remain debated. Understanding of the environment in which chalcedony forms is largely hampered by the lack of chalcedony-hosted fluid inclusions. Our study reports for the first time fortuitously preserved, large-sized (up to 150 μm) fluid inclusions in chalcedony from the Gonchak deposit of optical calcite in the Early Triassic basalts belonging to the Siberian large igneous province. The application of microthermometric methods, scanning electron microscopy with cathodoluminescence, and laser Raman spectroscopy to the fluid inclusions and their host chalcedony recognized the formation of chalcedony from a colloidal suspension. The fluid inclusions represent a gel-like saline aqueous fluid that is residual after precipitation of spherulitic chalcedony aggregates with numerous H2O-bearing and H2O-poor layers. We propose that the colloidal nature of fluids forming chalcedony lends strong support to the natural existence of experimentally predicted “silicothermal fluids”. Such fluids can be instrumental in mobilizing and transporting large quantities of both silica and nano- and micro-particles of ore minerals, followed by efficient separation of the latter from coagulating silica gel into ore-rich zones and bodies.