Environmental conditions have a notable impact on clay minerals, primarily because of the chemical reactions they undergo with their immediate environment. These reactions are more pronounced in hot and humid tropical regions, and therefore, the study of clays deposited at the bottom of lakes in tropical regions can yield valuable insight into past environmental conditions. Here we present multiproxy records, including physical (magnetic susceptibility, grey-scale level and grain size), mineralogical (X-ray diffraction, Simultaneous Thermal Analysis, Fourier-Transform Infrared Spectroscopy), and geochemical (elemental composition by XRF-core scanner, organic geochemistry by IRMS) data, from three 210Pb-dated sediment cores (spanning recent centuries < CE 1470) retrieved from crater lakes Los Espinos, Tacámbaro and Teremendo in the Trans-Mexican Volcanic Belt (TMVB), central Mexico. The mineralogical results showed that disordered kaolinite, formed by hydrolysis and hydrothermal alteration, was the predominant mineral in the sediments of the three lakes. The abundance of kaolinite changed in line with organic carbon and organic matter-related elements (Br, S and Ni) and showed opposite trends with lithogenic elements (Ti, K, and Fe). The geochemical data further suggested that increases in kaolinite abundance are linked to the formation of organo-mineral aggregates related to periods of elevated lake productivity that in turn may reflect lake level changes in the closed basins. In Lake Tacámbaro, following the construction of a canal in the early 20th century and subsequent regulation of lake level, the relationship between organic material and kaolinite was no longer present