Understanding clay-mineral assemblages forming in saline lakes aids in reconstructing paleoenvironments on Earth and other terrestrial planets; this is because authigenic phyllosilicates are sensitive to the prevailing geochemical conditions present during formation. In most geochemical models, evaporative concentration favors sepiolite with increasing silica and Mg2+ concentrations without considering the role of the biogenic removal of silica from solution by diatoms. In the present study, phyllosilicates occurring in the mudflats of Bolivian salars were investigated to aid in understanding the geochemical factors that control mineral assemblages forming in (SO42–)- and (Cl–)-rich environments in relation to dissolved silica. From transects across the mudflats, the physical, chemical, and mineralogical characteristics of the bulk sediment and the <2 μm fraction of each sedimentary layer were analyzed. From these analyses, three types of sediments were identified: (1) regolith sediments dominated by Al-dioctahedral smectite, illite, and chlorite; (2) detritus-rich mudflat sediments with Mg-trioctahedral smectite and Al-dioctahedral smectite along with illite and chlorite; and (3) authigenic mudflat sediments dominated by poorly formed Mg-trioctahedral smectite, kerolite, and biogenic silica. The absence of sepiolite-palygorskite in the salars is the result of excessively high Mg:Si ratios within the waters. In the surface water Mg becomes enriched relative to Si as diatoms remove dissolved Si from solution through biologically mediated uptake. The geochemical conditions present within the salars that act to preserve the diatom frustules and prevent their dissolution include: neutral–slightly alkaline pH solutions, cold temperatures, shallow water, and high salinity. Under these conditions the formation of sepiolite is restricted by the small amount of dissolved silica, despite the silica-rich environment. The formation of Mg-smectite and kerolite is favored under these conditions.