Geothermometrical characterisation of low-temperature, carbonate-evaporitic geothermal systems is usually hampered by the lack of appropriate mineral equilibria to successfully use most of the classical geothermometers and/or by the thermodynamic uncertainties affecting some of the most probable mineral equilibria in low temperature conditions. This situation is further hindered if the thermal waters are additionally affected by secondary processes (e.g., CO2 loss) during their ascent to surface. All these problems cluster together in the low-temperature Alhama-Jaraba thermal system, hosted in carbonate rocks, with spring temperatures about 30 degrees C and waters of Ca-Mg -HCO3/SO4 type. This system, one of the largest naturally flowing (600 Vs) low temperature thermal systems in Europe, is used in this paper as a suitable frame to assess the problems in the application of chemical geothermometrical techniques (classical geothermometers and geothermometrical modelling) and to provide a methodology that could be used in this type of geothermal system or in potential CO2 storage sites in similar aquifers. The results obtained have shown that the effects of the secondary processes can be avoided by selecting the samples unaffected by such processes and, therefore, representative of the conditions at depth, or by applying existing methodologies to reconstruct the original composition, as is usually done for medium to high temperature systems. The effective mineral equilibria at depth depend on the temperature, the residence time and the specific lithological/mineralogical characteristics of the system studied. In the present case, the mineral equilibria on which classical cation geothermometers are based have not been attained. The low proportion of evaporitic minerals in the hosting aquifer prevents the system from reaching anhydrite equilibrium, otherwise common in carbonate-evaporitic systems and necessary for the specific SO4-F geothermometer or the specially reliable quartz (or chalcedony) - anhydrite equilibrium in the geothermometrical modelling of these geothermal systems. Under these circumstances, the temperature estimation must rely on quartz (or chalcedony), clay minerals and, especially, calcite and dolomite. However, clay minerals and dolomite present important thermodynamic uncertainties related to possible variations in composition or crystallinity degree for clays and order/disorder degree for dolomite. To deal with these problems, a sensitivity analysis to the thermodynamic data for clay minerals has been carried out, comparing the results obtained when considering different solubility data. The uncertainties associated with dolomite have been addressed by reviewing the solubility data available for dolomites with different order degrees and performing specific calculations for the order degree of the dolomite in the aquifer. This approach can be used to find the most adequate dolomite thermodynamic data for the system under consideration, including medium-high temperature geothermal systems. Finally, the temperature estimation of the Alhama-Jaraba waters in the deep reservoir has been obtained from simultaneous equilibria of quartz, calcite, partially disordered dolomite and some aluminosilicate phases. The obtained value of 51 +/- 14 degrees C is within the uncertainty range normally affecting this type of estimations and is coherent with independent estimations from geophysical data.