Interpreting the environmental conditions under which ancient microbialites formed relies upon comparisons with modern analogues. This is why we need a detailed reference framework relating the chemical and mineralogical compositions of modern microbialites to the physical and chemical parameters prevailing in the environments where they form. Here, we measured the chemical, including major and trace elements, and mineralogical composition of microbialites from ten Mexican lakes as well as the chemical composition of the surrounding waters. Saturation states of lakes with different mineral phases were systematically determined and correlations between solution and solid chemical analyses were assessed using multivariate analyses. A large diversity of microbialites was observed in terms of mineralogical composition, with occurrence of diverse carbonate phases such as (Mg-)calcite, monohydrocalcite, aragonite, hydromagnesite, and dolomite as well as authigenic Mg-silicate phases (kerolite and/or stevensite). All lakes harbouring microbialites were saturated or supersaturated with monohydrocalcite, suggesting that such a saturation state might be required for the onset of microbialite formation and that precursor soluble phases such as amorphous calcium carbonate and monohydrocalcite play a pivotal role in these lakes. Subsequently, monohydrocalcite transforms partly or completely to aragonite or Mg-calcite, depending on the lake (Mg/Ca)aq. Moreover, lakes harbouring hydromagnesite-containing microbialites were saturated with an amorphous magnesium carbonate phase, supporting again the involvement of precursor carbonate phases. Last, authigenic Mg-silicates formed by homogenous or heterogenous nucleation in lakes saturated or supersaturated with a phase reported in the literature as “amorphous sepiolite” and with a H4SiO4 concentration superior to 0.2 mM. A strong correlation between the alkalinity and the salinity of all the lakes was observed. The observed large variations of alkalinity between the lakes relate to varying concentration stages of an initial alkaline dilute water, due to a varying hydrochemical functioning. In all cases, the size of microbialites in the lakes correlated positively with salinity, (Mg/Ca)aq ratio and alkalinity. The trace element compositions of the microbialites also varied significantly between the lakes. Detrital contamination of the studied microbialites was the major factor affecting their rare earth elements (REE) + Y patterns. In particular, the microbialites highly affected by detrital contamination showed a high (REE + Y) content and flat (REE + Y) patterns. In contrast, some microbialites poorly affected by detrital contamination showed (REE + Y) patterns with features commonly reported for marine microbialites, such as a superchondritic Y/Ho ratio, enrichment in heavy REE and a negative Ce anomaly. This last observation questions the possibility to infer the marine versus lacustrine origin of a microbialite based on (REE + Y) patterns only. Overall, while microorganisms can impact nucleation processes and textural arrangements in microbialites, we observe that the hydrogeochemical evolution of lakes exerts a primary control over the onset of microbialite formation and the evolution of their chemical and mineralogical composition. Moreover, while changes of all these chemical and mineralogical features upon diagenesis and metamorphism will need to be assessed, the present study, together with recent meta-analyses of modern microbialites, broadens the set of modern references available for comparisons with geological archives.