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Abstract Drilling of the Gotthard Rail Base Tunnel through the Central Alps from 2005 to 2010 opened up fractured basement units and frequent water inflows provided access to the major fluid-rock interactions processes in orogenic crystalline upper crust. Construction of the 57 km long tunnel was divided into five different sections. Here we report data and observations from the 10 km long central Sedrun section 211 water samples were collected at inflow points 900 to 2350 m below the surface. The exceptional samples and data provide a comprehension of the hydrochemical evolution and solute acquisition of deep groundwater in basement units. The investigated tunnel section drilled through steeply dipping rock units and vertical fracture systems at high angle. It cuts across granite, gneiss and schist of the pre-Alpine basement and across two narrow zones of meta-sediments. Rock temperature along the Sedrun section varies from 30 to 45 °C depending on the thickness of the overburden. The fracture water is of meteoric origin and acquires its composition exclusively by chemical interaction with the surrounding rocks along the flow path. Water from inflow points in the basement of the Gotthard Massif has typically a high pH of about 10 and total dissolved solids in the range of 100 to 300 mg L−1. Sodium is the prime cation of most waters. Although plentiful in the rocks, calcium, potassium and magnesium are low to very low in water. The anions associated with Na are carbonate/bicarbonate, sulfate, fluoride and chloride in widely varying proportions. High fluoride concentrations of up to 15.4 mg L−1 are characteristic for most waters. As a result of the high pH dissolved silica (SiO2) reached concentrations of up to 58 mg L−1 and represents 25—30 wt% of the solutes. The meteoric recharge provides dissolved O2 and CO2 to the fluid-rock interaction processes. The solutes derive from the dissolution of feldspar (Na+, SiO2aq), oxidation of sulfides to sulfate (SO4 2−), alteration of biotite (F−), and fluid inclusions opened by brittle deformation (Cl−). The solids formed during fluid-rock interaction, mainly zeolites, chlorite (and other clay minerals) and secondary Fe-minerals, remove Mg, Fe, and K almost quantitatively from the water. The high pH results from hydrolysis of silicates. The data distinctly show that within the depth interval of 1.0–2.5 km below surface deep water in continental basement evolves to a low TDS, high pH, sodium carbonate and silica solution by interaction of gneiss and granite with infiltrating pristine meteoric water, snow and rain.