Tropical lakes experience less thermal convection than temperate lakes and can be stably stratified by temperature gradients alone. Deep tropical lakes are often presumed meromictic, but conditions for sustained meromixis are poorly constrained. Here, we investigate the stratification stability of a deep (200 m) tropical Lake Towuti (Indonesia) and analyze its sensitivity to meteorological and climatic parameters using exploratory hydrodynamic simulations. The inferred effects on water chemistry are further evaluated with a reactive-transport biogeochemical model. In contrast to the previous assumption of meromixis, our results suggest that in 2008 Lake Towuti experienced mixing over most of its water column, with the attendant weak oxygenation of the previously anoxic lower strata. The lake likely remained stratified afterwards, but the chemical distributions measured after the episode, particularly during the International Continental Scientific Drilling Program in 2015, were out of steady state, and may be still evolving in time. We find the thermal stratification to be most sensitive to average air temperatures and wind speeds and predict further stabilization of the lake by climate change. We also describe a negative feedback mechanism that can stabilize oligomictic tropical lakes for a number of years after the episodes of mixing and cooling, and infer that such episodes should be significantly less frequent in deeper lakes.