Physical processes play important roles in controlling eutrophication and oligotrophication. In stratified lakes, internal waves can cause vertical transport of heat and nutrients without breaking the stratification, through boundary mixing events. Such is the case in tropical Valle de Bravo (VB) reservoir lake, where strong diurnal winds drive internal waves, boundary mixing, and hypolimnetic warming during stratification periods. We monitored VB during 21 years (2001–2021) when important water-level fluctuations occurred, affecting mixing and nutrient flux. Stability also varied as a function of water level. Hypolimnetic warming (0.009–0.028◦ C day−1) occurred in all the stratifications monitored. We analyzed temperature distributions and modeled the hypolimnion heat budget to assess vertical mixing between layers (0.639–3.515 × 10−6 m3 day−1), vertical diffusivity coefficient KZ (2.5 × 10−6 –13.6 × 10−6 m2 s−1), and vertical nutrient transport to the epilimnion. Nutrient flux from the metalimnion to the epilimnion ranged 0.42–5.99 mg P m−2 day−1 for soluble reactive phosphorus (SRP) and 5.8–101.7 mg N m−2 day−1 for dissolved inorganic nitrogen (DIN). Vertical mixing and the associated nutrient fluxes increase evidently as the water level decreases 8 m below capacity, and they can increase up to fivefold if the water level drops over 12 m. The observed changes related to water level affect nutrient recycling, ecosystemic metabolic balance, and planktonic composition of VB.