There is growing interest in geothermal energy, which is considered as an efficient energy solution to mitigate rising atmospheric CO2. Besides known high enthalpy geothermal systems, increasing attention is paid to low temperature geothermal systems, as they are suitable for local use. Although geothermal production seems to be an environmentally advantageous renewable energy, it might result in significant CO2 emissions. In this study, we investigate the relationship between temperature, fugacity of CO2 (fCO2), and mineral buffers in the reservoir conditions, taking the low- to medium- enthalpy thermal waters in the Central Betic Cordillera as case study. Using geochemical modeling, three main groups of waters have been identified depending on temperature, buffering mineral assemblage, and fCO2 in their reservoir. A group of waters with a reservoir temperature ranging from 70 to 90 °C and located in the intramountain sedimentary basins shows a fCO2 in depth ranging from ~6 × 10−2 and 6 × 10−1. The reservoir chemistry of this water group seems to be mainly controlled by carbonates and evaporites displaying a fCO2 variation between depth and surface (ΔfCO2) of 10−1. Another intermediate group of waters, located in an active extension zone, displays lower temperature (50–60 °C) and fCO2 in the reservoir (from 10−3 to 10−2). Finally, the third group of waters, located on the metamorphic complexes contacts, show the highest estimated temperatures (130–140 °C) and fCO2 in the reservoir (1 to 102). The two latter groups suggest increasing buffering effect of alumino-silicates, in addition to carbonates and quartz. Therefore, we evidenced a strong relationship between temperature and fCO2 in the reservoir as well as the potential mineral buffers. We discussed the potential of geothermal systems as clean energy source based on the estimation of the CO2 emissions generated by the investigated thermal systems for a practical case of household heating.