Stable isotopic (dD and d18O) data indicate about 13% total evaporative concentration has occurred in Yellowstone Lake, yet lake waters are enriched in dissolved As, B, Cl, Cs, Ge, Li, Mo, Sb, and W by at least an order-of-magnitude relative to the flow-weighted composition of inflowing streams. We conclude that lake water is a mixture of inflowing surface water and hydrothermal source fluid that is strongly enriched in Cl and other elements. We estimate that ~10% of the total hydrothermal flux in Yellowstone National Park (YNP) occurs in Yellowstone Lake. Geochemical and mineralogical studies of hydrothermal deposits and hydrothermally altered lake sediments (vent muds) from the active or recently active vent sites on the floor of Yellowstone Lake indicate that their formation is due to hydrothermal fluid quenching during flow through shallow conduits, or to mixing upon egress into cold bottom waters. Siliceous precipitates form conduits within the uppermost sediments, tabular deposits along sedimentary layers, and spires up to 8 m tall. These deposits are enriched in As, Cs, Hg, Mo, Sb, Tl and W. Spires, vent deposits, and conduits contain filamentous microstructures that probably represent silicified bacteria. Partly recrystallized and silicified diatoms are abundant in deposits below the sediment-water interface. Vent muds and some outer conduit walls show pervasive leaching of silica, which explains the occurrence of most sublacustrine vents in craters. Systematics of dD and Cl variations, as well as silica and cation geothermometry for hydrothermal fluids, suggest that ascending fluids boil due to depressurization to a temperature of ~220°C and then mix with pore waters prior to venting on the lake bottom. Depositional temperatures for sublacustrine silica deposits, calculated using oxygen isotope fractionation, range from 78°C to 164°C. The amorphous silica-saturated vent fluids precipitate silica to form spires or conduits largely by conductive cooling. Bacterial accumulations may have inhibited the mixing of vent fluids and bottom waters, and provided a site for silica deposition.