The Edremit pull-apart basin located on the southern branch of the North Anatolian Fault System hosts the Güre, Edremit, and Ayvalık geothermal areas. The graben faults that form the basin are regions of high hydraulic conductivity and contribute to the deep circulation of thermal water. In this study, the chemical and isotopic characteristics of thermal and cold waters in these fields are investigated by using the major ion and trace element contents as well as environmental isotope compositions. The Güre and Edremit thermal waters are of Na-SO4 and Na-SO4-HCO3 type and Ayvalık thermal waters are represented by Na-HCO3 composition. One of the thermal waters in the Ayvalık field is likely to experience seawater intrusion. The diversity in the chemical composition and temperature of the studied thermal waters is explained by a combination of processes including mixing of the thermal water with cold groundwater, feldspar dissolution and ion exchange in clayey rocks. Results of environmental isotope analyses indicate that the Ayvalık waters have a shallower circulation and are recharged from elevations lower than Edremit and Güre waters. The Karakaya formation and volcanic rocks comprise the recharge area of Ayvalık waters whereas Kazdağ group rocks and granites are the major lithologies exposing on the recharge area of Güre and Edremit fields. Since quartz geothermometers yield temperatures less than 190 °C, silica concentration in waters is controlled by the chalcedony phase. Reservoir temperatures estimated by the chalcedony geothermometer are 79–96 °C for Güre waters, 64–73 °C for the Edremit waters and 48–54 °C for the Ayvalık waters. Cation geothermometers yield temperatures that are significantly higher than the silica geothermometers, 65–126 °C, 65–117 °C and 38–99 °C for the respective fields. Mineral equilibrium calculations indicate that all waters show undersaturation with respect to sulfate minerals (anhydrite and gypsum) and chalcedony.