The surface geothermal water chemistry and alteration mineralogy associated with rhyolitic rocks at Torfajökull central volcano, Iceland was studied. The geothermal waters ranged in pH and temperature from 2.33 to 9.77 and 6–98°C, respectively, and was characterized by variable alteration products including amorphous silica, quartz, hematite, goethite, kaolinite, elemental sulfur, pyrite, anatase, montmorillonite. alunite, amorphous iron silicates, pyrite, goethite, hematite and illite. The chemical composition of these waters and the associated mineralogy is influenced by several processes occurring from the geothermal reservoir to the surface including boiling, mixing, degassing, oxidation and water–rock interaction. In order to quantify these processes and explain the observed geothermal surface water composition and mineralogy, a geochemical model was applied that involved three steps: (i) defining the composition of the end-member fluid types present in the system, (ii) applying a mixing model based on conservation of non-reactive elements and enthalpy (temperature) and (iii) quantifying the process of progressive fluid–rock interaction and secondary mineral formation in the surface zone. The model may be applied to any geothermal system. Geothermal waters at Torfajökull represent either a mixture of non-thermal water and condensed steam with insignificant fraction of boiled reservoir water or boiled reservoir water that has been mixed. Two types of steam-heated waters were observed, acid and carbonate rich, the difference thought to be related to the boiling process. Steam-heated carbonate waters are formed from <10% steam originated by boiling and phase segregation at >200°C followed by mixing with non-thermal water at shallow depth whereas steam-heated acid waters are formed upon extensive boiling and steam condensation and mixing with non-thermal surface in the surface zone. The surface alteration mineralogy and associated elemental mobility is largely influenced by the formation mechanism and chemistry of the geothermal surface water in the surface zone. At acid pH and under oxidized conditions Na, K, Mg and Ca were observed to be mobile and leached out whereas Fe, Ti and to a less extent Si, were retained in the alteration product forming amarphous silica, kaolinite, anatase and pyrite as well as some smectites and sulfates. For steam-heated carbonate waters, Na and K were observed to be mobile whereas Fe and Si are retained in amorphous silica, ferrihydrites and iron rich silicates. Carbonates were not calculated or observed to form associated with carbonate springs. Magnesium, Ca and K were observed to be mobile at pH<6 whereas they are quantitatively retained into smectites and eventually also zeolites and carbonates with increasing pH. As a consequence, the mobility of Mg and K and to a less extent Ca and Na are greatly reduced under alkaline conditions. Based on the above, the key factors controlling the fluid–rhyolite interaction under surface geothermal conditions (∼100°C) are acid supply, oxidation state and extent of reaction. The surface geochemical exploration methods developed and applied here are suitable for any geothermal system in order to explore geochemical processes occurring in active geothermal systems including boiling and fluid mixing, fluid and elemental sources, reservoir fluid properties and when applied before and during geothermal exploitation and utilization how these may have changed in nature with time.