Increasing droughts and related water losses challenge lake systems. We analyzed water and sediment samples from five lakes in five subsequent dry and rainy seasons to study lakes’ vulnerability at times of significant environmental change, and to revisit the “old question” of whether different tropical lake water types can be observed in more complex datasets to better understand their limnological status, differences between lake types, and to broaden their baseline database for subsequent research. High temperatures combined with reduced oxygen levels (<<80% saturation) impose challenging boundary conditions for all biotas. Clearwater, black-, and whitewater can be differentiated by their signatures in dissolved ions, dissolved organic carbon, and selected major, minor and trace elements in water and sediment. Lake waters resembled remote rainwater. Lake sediment composition was compared with that of ‘terra firme’ soils in surrounding catchments for 47 chemical elements including carbon and nitrogen, macro- and micronutrients. With few exceptions (Ti; REE), sediment element concentrations showed mostly depletion when compared to the upper continental crust, reflecting regional soil chemistry and ongoing depletion of surrounding soils due to deforestation and changing landcover. Sediments act as intermediate sinks for eroded soil materials and show increasing buffer capacity from clearwater < blackwater < whitewater lakes. Under conditions of climate change, especially in areas close to the equator, the already pronounced oxygen depletion will pose further challenges for aquatic life. Lake, pisciculture, and catchment management should be adapted accordingly.