Abstract Thermodynamic modeling of equilibria in the system water–rock–organic acids was used to study the influence of organic acids on Ca and Mg redistribution between a solution and a solid phase in connection with the use of calcites of variable composition CaxMg1–xCO3 as indicators of paleoclimatic environments. In the thermodynamic model, high-molecular humic substances (fulvic + humic acids) were represented by a set of independent metal-binding centers. Therefore, their number was preset based on the given density of proton- or metal-binding sites. The numerical implementation of several geochemical situations involving the dissolution/deposition of calcites with different Mg contents showed that the main effect of fulvic and humic acids is the acidification of solutions and the reduction of carbonate stability. Although humic substances can play an important role in fixing Ca and Mg and removing them from solution, their actual concentrations in natural media (<<1 g/L) do not cause significant changes in the composition of CaxMg1–xCO3 phases. On the other hand, there is quantitative evidence that variations in the Mg/Ca ratio in a solution and a solid phase are significantly influenced by the evaporative concentration of Mg-oversaturated solutions, alkalization/acidification during their evolution, or CO2 content variations owing to changes in climate and lake activity.