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Water transparency (represented by Secchi disk depth, SDD), a key physical feature of lake ecosystems, is directly controlled by optically active substances, including organic matter (concentration and composition) and phytoplankton biomass which are closely related to eutrophication and climate warming. Here, we examined the trends in SDD variation and the driving mechanisms based on short-term (35 lakes, JulySeptember 2017) and long-term (3 lakes, 19822016) datasets covering lakes with different trophic states on the Yunnan Plateau. In the short-term dataset, increases in organic matter content, phytoplankton biomass and trophic state reduced the SDD. In the long-term dataset, the annual SDD decreased significantly in all three lakes. Significant increases occurred in phytoplankton biomass in eutrophic Lake Dianchi, both phytoplankton biomass and organic matter content in oligo-mesotrophic Lake Erhai, and organic matter content in oligotrophic Lake Fuxianhu over time, and these increases were related to increased trophic state (or change in nutrient level) and/or possibly to climate warming. Furthermore, phytoplankton biomass and organic matter content were important direct driving factors for reduced SDD in eutrophic Lake Dianchi and oligotrophic Lake Fuxianhu, respectively, while the interaction of these two factors was the most important factor in oligo-mesotrophic Lake Erhai. These results implied that eutrophication and climate warming could regulate SDD by changing organic matter concentration and/or phytoplankton biomass, which may depend on the lacustrine trophic state. However, further studies across larger geographical scales and more lakes are needed to confirm these results.