Over the last 70 years, stable isotopes have provided critical insight into the processes governing transfer of mass and energy through geologic systems. Significantly, isotopic signals in minerals reflect conditions of crystallisation, and subsequent alteration history. In hydrothermal systems, isotope tools have been applied to interpret fluid origin, temperature, and interaction with host rock. The research carried out here makes use of emerging techniques to measure hydrogen, oxygen, carbon, and clumped isotopes in carbonates and hydrous minerals. This work encompasses three themes: (i) Development of new laser spectroscopy approaches for measuring δ2H and δ18O in hydrous minerals (ii) Testing carbonate clumped isotope thermometry in geothermal fields and mineral deposits (iii) Application of carbonate and hydrous mineral isotope tools in epithermal precious metal deposits A novel approach to measure δ2H and δ18O in hydrous minerals is presented in Chapters 3-4. Measurement was carried out on phyllosilicates, hydrous sulphates, and multimineralic whole rock assay pulps using a custom-built thermal dehydration-dehydroxylation Off-Axis Integrated Cavity Output Spectroscopy (TD-OA-ICOS) system. The δ2H methodology presented is equal to isotope ratio mass spectrometry in terms of speed and precision, but considerably lower in cost. This work represents the first hydrogen isotope measurements made by a laser spectroscopy system for serpentine, muscovite, sericite, talc, and biotite. The TD-OA-ICOS method was subsequently applied to measure δ18O in microvolumes of water, gypsum hydration water, and the hydroxyl component of phyllosilicate minerals (Chapter 4). Intramineral oxygen isotope fractionation values in kaolinite and muscovite, determined by comparison of δ18OOH measured by TD-OA-ICOS with δ18Osilicate measured by fluorination, are similar to existing constraints. Refinement of this approach should be carried out to test the relationship between formation temperature and intramineral oxygen isotope fractionation in clay minerals. TD-OA-ICOS was applied to reconstruct δ2H in well-constrained epithermal areas, exemplified by case studies at the Comstock Lode, USA (Chapter 4) and Miocene-aged adularia-sericite Au-Ag deposits at Waihi and Karangahake on the North Island (Chapter 6). Taking mineral-specific fractionation factors into account, whole rock hydrogen isotope measurements indicate relatively homogeneous fluids of meteoric origin were involved in alteration at each deposit. Accurate reconstruction of fluid δ2H requires constraints upon the balance of illite and chlorite in samples. Mineral δ2H is useful for fingerprinting paleo latitude or altitude of source fluids, as evidenced by results from Comstock, which were ~60 ‰ lower for δ2H, relative to Waihi and Karangahake. It is apparent that mineral δ2H has greater utility towards understanding mixing in systems where fluids are isotopically distinct. The low cost, safety, and simplicity of operation of TD-OA-ICOS should also make the method attractive for manufacturers and regulatory agencies wishing to use hydrogen and oxygen isotopes to determine the geographic origin of consumer products containing hydrous minerals. Paleotemperature constraints around ore deposits are essential for characterising the relationship between advection, fluid circulation, and metal transport. In Chapter 5, carbonate clumped isotope thermometry (Δ47) is applied to identify temperature gradients in geothermal fields and hydrothermal ore deposits. This technique, based on quantification of thermodynamically sensitive 13C-18O bond abundance in carbonates, provides new capability to determine fluid δ18O, overcoming a problem which has undermined interpretation of carbonate isotope data in hydrothermal settings for more than 60 years. Geothermal fields (Wairakei, Ngatamariki, Broadlands-Ohaaki) in the Taupo Volcanic Zone, New Zealand served as natural laboratories to test the validity of clumped isotope calibrations in high temperature settings up to 300 °C. Taking local fluid δ18O into account, results indicate modern TVZ calcite precipitated in equilibrium with produced geothermal waters. The clumped isotope technique was subsequently applied in epithermal (Waihi, NZ), skarn (Antamina, Peru), and carbonate-hosted (Mount Isa, Australia) metal deposits. Results highlight the potential for clumped isotopes to delineate the heat footprint around mineral deposits that contain carbonates. Further refinement of the clumped isotope method offers new potential to evaluate characteristics of ore deposit genesis, with respect to temperature, fluid source, and depth. This will prove especially useful in enigmatic carbonate-hosted hydrothermal settings, where temperature and hydrology are unresolved. Paired oxygen isotope and carbonate clumped isotope measurements at Waihi demonstrate that δ18O of hydrothermal calcite is primarily influenced by rock temperature, with variation in fluid composition due to water-rock exchange exerting secondary control. While calcite precipitates both in and out of phase with precious metals in epithermal areas (e.g. Waihi), clumped isotope signals reflect the overall thermal structure, providing a new avenue to identify hotter upwelling zones, where boiling drives deposition of Au, Ag and other metals. Ultimately, the findings presented herein are useful to workers in hydrothermal settings, with interest in mineral exploration and geothermal resource development, and are broadly applicable across the geologic sciences in topics ranging from paleoenvironmental studies to interpretation of basin histories.