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This study aimed to evaluate the importance of physical, chemical and biological factors (e.g., chlorophyll-a, and carbon) in the regulation of the summer epilimnion thickness (Zmix) of the tropical lakes focusing on trends of the current environmental variability. We sampled a set of tropical lakes from the middle Rio Doce lacustrine system (Minas Gerais, Brazil) for two consecutive summers. Besides Zmix, we analyzed the visible light attenuation (Kd(PAR)), dissolved organic carbon (DOC), chlorophyll-a (Chl-a), total suspended solids (TSS), and fetch. We also analyze the quality of the dissolved organic matter (DOM) through colored dissolved organic matter (CDOM), spectral slope (S), DOC-specific absorbance (SUVA) and the ratio between the absorbance at 250 nm and 365 nm (E-250:365). Our results showed quite different results during the two years studied. In the summer of 2012, when there was higher rainfall, variations in Zmix were correlated to the optical factors associated with DOM quality, while in the drier summer of 2013 Chl-a, TSS and fetch were the variables that more explained Zmix. It suggests that DOM regulates the Zmix in the rainy periods in the studied tropical lakes and that control is determined by the balance between the DOM input (runoff) and output (such as photodegradafion) of the aquatic systems. In reduced rain conditions (summer 2013), the factors responsible by chemistry photodegradation of DOM were predominant, and the organic matter was no longer controlling Zmix, which was driven by internal mixing, productivity, and the wind (Chl-a, TSS and fetch). In this study we showed how changes in precipitation might cause shifts in the factors that regulate the epilimnion thickness in tropical lakes.