The Indonesian seas contain evidence of enhanced vertical mixing. Coupled with the highly stratified tropical thermocline, this enhanced mixing implies large vertical fluxes of heat and buoyancy from the ocean-atmosphere boundary downward deep into the water column. To accurately predict climate change requires quantifying this vertical mixing and its temporal and spatial variability, because these fluxes help regulate ocean heat storage and thermohaline circulation. We use 18 years of temperature stratification data from expendable bathythermographic (XBT) probes to show that the finestructure associated with mixing reveals clear enhancement near topography and significant temporal variability. We observed a 33 percent decrease in finestructure in the upper water column during El Niño years, suggesting reduced mixing, whereas during La Niña years, an 18 percent increase in finestructure suggested enhanced mixing.