This study characterizes the hydrochemistry and geochemical signature of the Upper Cretaceous geothermal aquifer in the Zharkunak zone (Eastern Ili Depression, SE Kazakhstan) using certified analytical datasets from five deep wells (5539, 1-RT, 3-T, 1-TP, and 2-TP). The waters are hyperthermal (89–103 °C), alkaline (pH 8.1–9.0), and weakly mineralized (TDS 0.3–1.0 g/L), with sodium-dominated facies ranging from Na–HCO₃–SO₄ to Na–SO₄–Cl. Hydrochemical analysis indicates that water–rock interaction and cation exchange are the primary controls on fluid evolution, with limited influence from evaporation or external salinity sources. Elevated fluoride (up to ~10 mg/L) and dissolved silica (H₂SiO₃, often >50 mg/L) reflect prolonged high-temperature interaction with silicate-rich lithologies under low Ca²⁺ conditions. Trace elements and radon activity (up to 0.32 nCi/L) further support deep, fault-controlled circulation pathways. PHREEQC modeling indicates near-equilibrium to slight supersaturation with respect to silica phases, suggesting a potential risk of silica scaling during cooling, while carbonate scaling remains limited. Although the dataset is based on discharge conditions from a limited number of wells, the results demonstrate that the Zharkunak system has strong geothermal utilization potential, with management considerations related to fluoride, radon, and silica scaling. Future work should focus on integrating isotopic analyses and reactive transport modeling to better constrain subsurface processes and long-term system behavior.