In this study, we investigate chemical and isotopic characteristics of thermal waters of the Emir geothermal field in the Kula region, which hosts the youngest volcanism in Turkey. Studied thermal waters with temperature and electrical conductivity values of 21–63 °C and 3840 to 5210 μS/cm are of Na–HCO3 type and have neutral character. δ18O and δD of thermal waters are − 9.40 to − 8.41‰ and − 64.16 to − 56.38‰ (VSMOW) and indicate a meteoric source with local recharge. Tritium values of thermal waters in the Emir geothermal field are mostly < 1 TU signifying a deep circulation. Positive δ13C values (1.32–4.46‰ VPDB) imply that carbon is derived dominantly from marine limestone and dominantly from endogenic CO2. δ18O and δ34S of dissolved sulfate yield that marine limestone is the source of sulfur in thermal waters, which are partly affected by sulfide oxidation and bacterial reduction processes. At discharge temperatures, Emir thermal waters are oversaturated with respect to albite, aragonite, calcite, α-cristobalite, dolomite, gibbsite, illite, K-feldspar, kaolinite, muscovite and quartz but undersaturated for anhydrite and wairakite. The activity diagrams suggest that high Na+ and K+ concentrations in waters are attributed to dissolution of muscovite, K-feldspar and albite. Chemical and isotopic compositions of the Emir thermal waters are controlled by a combination of processes including water–rock interaction, dissolution/precipitation and ion exchange. Various chemical and isotopic geothermometers applied to the thermal waters yielded reservoir temperatures in the range of 80–125 °C. Paleo-temperatures estimated from δ18O values of travertines and thermal waters (isotope fractionation) are consistent with modern discharge temperatures.