In the Southern Volcanic Zone of Chile (SVZ, 33-46 degrees S) the interaction between regional fault systems and volcanic centers forms high enthalpy geothermal systems. This study aims to understand the hydrogeochemical processes (e.g., water mixing and water-rock interaction) that control the sources and distribution of Li, B and Sr in geothermal conditions. We selected two high-enthalpy hydrothermal systems that host diverse geothermal features, including boiling springs, fumaroles and geysers: Alpehue and Puyehue-Cordon Caulle. We used a combination of geochemical and isotopic methods, including stable isotopes of lithium (delta Li-7), boron (delta B-11) and strontium (Sr-87/Sr-86) in a set of samples from thermal emissions, river waters and volcanic rocks. We analyze the potential sources of dissolved boron, lithium and strontium, and the hydrogeochemical processes that control their behavior in the systems. At Alpehue, geothermal fluids showed isotopic compositions (delta Li-7 approximate to +0.5 parts per thousand, delta B-11 approximate to -3.3 parts per thousand) similar to those in volcanic rocks (delta Li-7 = +1.39 parts per thousand, delta B-11 = -2.2 parts per thousand), suggesting high-temperature water-rock interaction. At Puyehue-Cordon Caulle, the isotopic signal varies inside the large-scale volcanic system: at the steam-heated zone, composed of high temperature features (fumaroles and mud pools) and affected by argillic alteration, waters have boron isotopic signals similar to altered rocks (delta B-11 approximate to +15 parts per thousand), while lithium matched the signal of magmatic fluids (delta Li-7 approximate to -2.0 parts per thousand). In contrast, peripheral bicarbonate springs (T similar to 50 degrees C) indicate equilibrium with a deep neutral geothermal reservoir, showing the signal of fresh volcanic rocks (delta Li-7 approximate to +5.9 parts per thousand; delta B-11 approximate to -2.2 parts per thousand) but with very low Li and B concentrations due to mixing with cold surficial waters. The results support a model where geothermal water acquires the isotopic signal from the host rocks, with a variable contribution of magmatic fluids, which is enhanced in steam-heated water conditions. The multi- isotopic analysis conducted in this study identified three main processes controlling the distribution of Li, B and Sr: (1) heat-fluid-rock interaction, controlled by the isotopic signature of each hosting rock, (2) mixing with magmatic fluids, presumably influenced by regional fault systems, and (3) hydrothermal alteration, influencing rock leaching and imprinting its isotopic signature on thermal water.