The purpose of this study is to understand mineral diagenesis authigenic mineral and the effect of climate on mineral of Pleistocene-Holocene sediment deposits in the Southern Kenya Rift. Lake Magadi unique geologic settings are characterized by extreme alkalinity and high silica activities. The mineralogical analysis was achieved by X-Ray diffraction (XRD) and Scanning Electron Microscopy (SEM) applications. The bulk mineralogy (quartz, halite, calcite) is the same on all localities due to similar volcaniclastics compositions throughout the Kenya Rift Valley. The clay mineralogy significantly differ among the groups of sample localities. The differences reflect different tectonic settings and ambient climate regime. In humid climate at higher elevation detrital clay minerals are abundant (feldspars, phillipsite). At lower elevation like Lake Magadi, the clay fractions dominated by authigenic minerals (zeolites and silicate minerals found with zeolites). These results show the potential of clay minerals as terrestrial climate proxies.