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A conceptual model has been proposed based on water samples collected from geothermal springs in the Shyok suture zone of North-West Himalayas, Ladakh geothermal province, India by nurturing hydrogeochemistry, mineralogical insights, and stable isotopic (δD, δ18O) systematics. The reservoir rock is comprised of granitic segment with intrusion of volcano-plutonics and a variety of meta-sedimentaries which becomes more exposed towards western side of the valley in the form of Shyok Ophiolitic melange. Thermal waters, located above 3100 m above msl, with variable genetic classification (Changlung: Na–HCO3; Panamik: both Na–HCO3 and mixed type; Pulthang: purely mixed type), have TDS and temperature lying between 587 and 2278 mg/L and 28−78 °C, respectively. High concentration of trace elements (Li, B, As, Cs, Rb, W) in geothermal fluids points to the magmatic origin regarding their enrichment mechanism. Surface manifestation of hydrothermal/evaporitic minerals like thenardite, trona, sylvite, halite, nahcolite, thermonatrite, etc. establishes a signature of high-temperature at shallow level of reservoir and their dissolution kinetics decipher origin of solutes apart from weathering of alkali/alkaline aluminosilicates. Utilizing empirical chemical geothermometry and Si-Enthalpy mixing modelling, the estimated reservoir temperatures exhibit significant variability ranging from 100 to 210 °C and reservoir silica concentration 382 mg/L with average circulation depth of geothermal waters around 1.8 Km and fluid residence time of 2640 years. The Shyok-Nubra springs liberate substantial amount of CO2-enriched water, with degassing flux of 6.26 × 105 mol of CO2/year. δD and δ18O systematics reveal that geothermal springs are recharged by meteoric water, snow-melt and magmatic fluid with cold-water component of 27.1–62.4% mixed with hot fluids. Thermal springs are recharged from a single reservoir source located a shallow level towards North-West of Changlung having large lateral flow of about 25 Km generating Panamik and Pulthang fluids with subsequent dilution. This study highlights the extent and consequences of water–rock interaction across diverse lithologies (granite and mafic volcanics) in the Himalayas, emphasizing its implications over fluid circulation time and subsurface temperature considerations which rationalizes the evolution of geothermal fluids.