This study presents the first regional hydrogeochemical portrait of the mineral waters and associated gases of the Central Asia region, shaped by the Tien Shan and the Pamir. A geochemical survey of more than 50 fluid discharges from the Northern Tien Shan to the Pamir was carried out between 2018 and 2019. Isotopic (δD, δ18O, d15N2, d13CCO2, d13CCH4) and chemical data allow elucidating fluid genesis and general evolution in the continental collision zone. Geothermometric estimations as well as the content of the chemical components in waters (Cl, Li, B, Br) and gases (N2, CO2) suggest that the studied waters are not related to the presence of any active hydrothermal systems at shallow depth. Silica and cation geothermometers along with thermodynamic equilibrium calculations indicate that the temperature of unmixed deep fluids does not exceed 110 to 150 °C. The determination of d15N2 and d13CCO2 has revealed that the mantle genesis of gas flux matches with the areas of CO2-rich waters manifestations. The dislocation of mineral and thermal waters of Central Asia along the major regional tectonic structures is provided by topographically driven and well-developed long circulation of waters at the depth of 1 to 4 km.