Chlorine, lithium, and boron are trace elements in rhyolite but are enriched in groundwater flowing through rhyolite because they tend to partition into the fluid phase during high‐temperature fluid‐rock reactions. We present a large data set of major element and δ³⁷Cl, δ⁷Li, and δ¹¹B compositions of thermal water and rhyolite from Yellowstone Plateau Volcanic Field (YPVF). The Cl/B, Cl/Li, δ³⁷Cl (−0.2‰ to +0.7‰), and δ¹¹B (−6.2‰ to −5.9‰) values of alkaline‐chloride thermal waters reflect high‐temperature leaching of chlorine, lithium, and boron from rhyolite that has δ³⁷Cl and δ¹¹B values of +0.1‰ to +0.9‰ and −6.3‰ to −6.2‰, respectively. Chlorine and boron are not reactive, but lithium incorporation into hydrothermal alteration minerals result​s in a large range of Cl/Li, B/Li, and δ⁷Li (−1.2‰ to +3.8‰) values in thermal waters. The relatively large range in δ⁷Li values of thermal waters reflects a large range of values in rhyolite. Large volumes of rhyolite must be leached to account for the chloride, lithium and boron fluxes, implying deep groundwater flow through rhyolite flows and tuffs representing Yellowstone's three eruptive cycles (∼2.1 Ma). Lower Cl/B values in acid‐sulfate waters result from preferential partitioning of boron into the vapor phase and enrichment in the near‐surface water condensate. The Cl/B, Cl/Li, δ⁷Li (−0.3‰ to +2.1‰), and δ¹¹B (−8.0‰ to −8.1‰) values of travertine depositing calcium‐carbonate thermal waters which discharge in the northern and southern YPVF suggest that chlorine, lithium, and boron are derived from Mesozoic siliciclastic sediments which contain detrital material from the underlying metamorphic basement.