Quartz formation processes in the Icelandic crust were assessed using coupled δ18O and δ30Si systematics of silica deposits formed over a wide temperature range (<150 to >550 °C). Magmatic quartz reveals δ18O (-5.6 to +6.6 ‰) and δ30Si (-0.4 ± 0.2 ‰) values representative of mantle- and crustally-derived melts in Iceland. Hydrothermal quartz and silica polymorphs display a larger range of δ18O (-9.3 to +30.1 ‰) and δ30Si (-4.6 to +0.7 ‰) values. Isotope modelling reveals that such large variations are consistent with variable water sources and equilibrium isotope fractionation between fluids and quartz associated with secondary processes occurring in the crust, including fluid-rock interaction, boiling and cooling. In context of published δ18O and δ30Si data on hydrothermal silica deposits, we demonstrate that large ranges in δ30Si values coupled to insignificant δ18O variations may result from silica precipitation in a hydrothermal fluid conduit associated with near-surface cooling. While equilibrium isotope fractionation between fluids and quartz seems to prevail at high temperatures, kinetic fractionation likely influences isotope systematics at low temperatures.